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pipeline.yaml
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__pipeline__:
name: tempe
main: main.j2
description: Rapid Human GRCh38 genomics suite
version: v1.2.2
bin: required_scripts/
constants:
tools:
base:
container: ghcr.io/tgen/containers/debian:bullseye
digest: b8f30ec0fb3f1c1ab0de63703b438f8476296df3097af5b52917ec7ce8417863
bcftools:
container: ghcr.io/tgen/containers/bcftools:1.17-23080313
digest: 29f46af18e1910acee183b7e8bed52543d38a84842f1d2477d6571952563aed4
bedtools:
container: ghcr.io/tgen/containers/bedtools:2.29.0-23080313
digest: cde92d1b69ecfda6e5f115c6b9220a312c380b0d7aa30378437476cd50206ee0
bpure:
container: ghcr.io/tgen/containers/b_pure:1.0.0
digest: 1360e309dc861cf8a70be88db69f22f2520273052444c055d913d4f8a96b9fd6
bwa_mem2_samtools:
container: ghcr.io/tgen/containers/bwa_mem2_samtools:2.2.1-23080315
digest: 98a83bc2d70fa39755a02c2d81de64ef36dac292cdf6b1fcf02570a3e227b7f6
cnvear:
container: ghcr.io/tgen/containers/cnvear:0.1.7
digest: 4a857e23b484ed0c32de5fb9356d427cd52ea141a797d443f453c457ab852ad2
deepvariant:
container: google/deepvariant:1.6.0-gpu
digest: 3b11b08770e4c2818fa65195b31267a430aac815652a7fc4bcd3a0e284a5368f
dle:
container: ghcr.io/tgen/containers/discordant_loci_extractor:0.1.6-24031215
digest: b644809bcc871bc633f43f4e311e0b872953a81f39812b124c97b504204b7282
expansion_hunter:
container: ghcr.io/tgen/containers/expansion_hunter:4.0.2-23080316
digest: 079db962be053c674c9e6673961b61a11342a8d7826d66dbaefe75902c60dbcb
fgbio:
container: ghcr.io/tgen/containers/fgbio:2.0.2-23082819
digest: c913496a731593eb173fe66a8b32d3071a4939f72a0403aecbe839ec6a29f94d
finalize:
container: quay.io/biocontainers/multiqc:1.13--pyhdfd78af_0
digest: db913f47894a386040d76ae5f46b19149a71377f5107327d15ec89d3a1ec3f5f
freebayes:
container: quay.io/biocontainers/freebayes:1.3.6--h6f59eb7_3
digest: 2f782d0d87c6c30097fd39694de3c4a52e840681dc27dd4cf3f87526b13abbba
gatk:
container: broadinstitute/gatk:4.4.0.0
digest: 044112d3d70603732d4a654ecaee33919cf9d45332d47268f5f1697b6ed558ed
gridss:
container: quay.io/biocontainers/gridss:2.13.2--h20b1175_1
digest: 886fe9d43ff1068edefe4a07ae8a04c061e2f8e8bcfb7708df9126ac24250562
gripss:
container: quay.io/biocontainers/hmftools-gripss:2.3.2--hdfd78af_0
digest: 4ac910852ddfa8156270b11826a533307024d261295243486a905dcd3fc257d6
hmmcopy:
container: quay.io/biocontainers/hmmcopy:0.1.1--h8b12597_4
digest: 607d8bd3fbe5627dd69f2b8f364cda06a672e5a0f20a29398a7092d2ab0f48d3
htslib:
container: ghcr.io/tgen/containers/htslib:1.17-23080709
digest: f468febb69a5412fa02990e9cdadbba97030d3e7eb27cc70343dac7d53919ee2
ichorcna:
container: quay.io/biocontainers/r-ichorcna:0.5.0--pl5321r43hdfd78af_1
digest: 51e8ff5f610fde81268d7ba3d4ae0905982675d8d5cce4e18fd24775afa6c431
lancet:
container: ghcr.io/tgen/containers/lancet:1.1.x-23080709
digest: acd89650b9389c748e1ec91eea7453301028b2a28a8059886793630096eeb74f
manta:
container: ghcr.io/tgen/containers/manta:1.6.0-23082819
digest: 8413ec3da1e20da9f0cc9544722c7e9d30135f4ee0aa8092b67fc74c782913a3
manta_tgen:
container: ghcr.io/tgen/containers/manta_tgen:1.6.0-23082819
digest: 01d5f283cecd53e2f8c5f96b2e39bf1190e59cb27b3b8ee54d2bf449ca78b3db
msisensor:
container: ghcr.io/tgen/containers/msisensor:1.1.a-23080815
digest: 304ae1828f574c5d5d8866d0530f35aa6c819fa17e3b7742b2539edde3b930c8
mutation_burden:
container: ghcr.io/tgen/containers/mutation-burden:1.2.4-23080815
digest: 8149ef5dbe66ba305082fc4ca486792e54371469189c46a774e23eec9312225e
octopus:
container: ghcr.io/tgen/containers/octopus:0.7.4-23080809
digest: 6ac2461140f82ab24d2a16815b7a697672c9aeb291de44f21e57b589f333ccf4
pairoscope:
container: ghcr.io/tgen/containers/pairoscope:0.4.2-23080810
digest: 0d6e622d19aa44f2cd21509d789881d9308412ee392ca42bdfeafdd8ea575f38
python3:
container: python:3.7.16-slim-bullseye
digest: a844c22fcd1f2b4bc945ed14e5148b2ca8fbe42c1685e8840a8200039ff04154
python3_with_modules:
container: ghcr.io/tgen/jetstream_containers/python:3.7.2-v1-with_modules
digest: 030adca9dc79c97178d00b65ab2dbd30e1b83f6163cad8204c66dc10868393e2
parabricks:
container: nvcr.io/nvidia/clara/clara-parabricks:4.0.0-1
digest: 0170beef24131a23bb63bc36ec059e493df1f04a4a78f9d2c5df9bce1d5d9a35
R:
container: ghcr.io/tgen/containers/r_with_modules:4.1.2-23080815
digest: 59b19f57dd510c520997df03ca5eaeb15a5c71db5637cdc834797964dd25a616
salmon:
container: combinelab/salmon:1.9.0
digest: 9c6fdc2e99967684fcc913d5ab5e9323169a7ec51da8f0068cb2cc0a94c84796
samtools:
container: ghcr.io/tgen/containers/samtools:1.17-23080815
digest: 859ff54d83f5dfd7b3ae2b3841f689efe4aa41ede9fb5f8df49bf648058ae0e3
samtools_with_python:
container: ghcr.io/tgen/containers/samtools_python:1.17-3.7.16-23082819
digest: 2eaadfb976fd23f3583c5ab35c536349243cfd6e015002434735667c6bd62ead
sigprofiler:
container: ghcr.io/tgen/containers/sigprofiler:0.0.24-24030411
digest: 4696efb66bdef231cbc64f145f777b847b47f6445444b30cd91713346f0c38ee
snpsniffer:
container: ghcr.io/tgen/containers/snpsniffer:7.0.0-23080810
digest: 93831227364dbe82f42836844e34ee7d33d798885edb5b98f5aaf7f13f360eb5
star_fusion:
container: trinityctat/starfusion:1.11.0
digest: a3f1bfbb3a7a3b501ecdd1cec4325d00516b73b504afac274d351d20deee44e4
strelka:
container: ghcr.io/tgen/containers/strelka:2.9.10-23080711
digest: e4c48b1470f2524da5734ebd84232446feec0e332b28e08c8997c3f21dffdc8e
subread:
container: quay.io/biocontainers/subread:2.0.0--hed695b0_0
digest: 97b2f544c6a8a1b209febcc23616fd77c46bdbb1d4f3005012456a380ca43d99
thred:
container: ghcr.io/tgen/containers/thred:1.1.0-23080712
digest: 615fa14c097a71bd11f6517acbfb334543764865636dc717bb680c4ca4cd8125
transparser:
container: ghcr.io/tgen/containers/transparser:1.0.1-23080810
digest: 2d9fdfd5700368ebe0f2512c154f18d7df3f9118c897eb46c117dc69eda2411d
trinity_bwa_samtools:
container: ghcr.io/tgen/containers/trinity_bwa_mem2:2.8.6-23082819
digest: b1f0623882ed2ac3a404dfd252732ae92fb1b9526ae9b9e6d367f08424d61500
vardict:
container: quay.io/biocontainers/vardict-java:1.8.3--hdfd78af_0
digest: 4069c082c97470bce4a07f228dbf74b6ea3fc5c4eaa93ba76d2826a496ca3c44
vcfmerger:
container: ghcr.io/tgen/containers/vcfmerger2:0.9.5-23090712
digest: 37640beed1f829702dbd8c03a1e4955a205abd8a38e209ea88ffa815c570a8fa
vcf2maf:
container: quay.io/biocontainers/vcf2maf:1.6.21--hdfd78af_0
digest: e33def318468ac924bdcc280c4aa8984865709d111cd0df9b0d82c7908b7dd07
vep:
container: ensemblorg/ensembl-vep:release_107.0
digest: f252df581820048dbc90229d38fbc7b94738743bd9ebc23ffcc533245e9ab0e5
verifybamid2:
container: griffan/verifybamid2:v2.0.1
digest: 2f1e33903d2b9a71b9feba061070cfbb16212a5a39420e10091500ec4b36fab8
tempe:
species: Homo sapiens
genome_build: grch38_hg38
genome_subversion_name: hg38_tempe
gene_model_name: ensembl_v103
gene_model_version: 103
canonical_cds_intervals: /home/tgenref/homo_sapiens/grch38_hg38/hg38_tempe/gene_model/ensembl_v103/Homo_sapiens.GRCh38.103.ucsc.cds_padded.final.bed
capture_kit_path: /home/tgenref/homo_sapiens/grch38_hg38/hg38_tempe/gene_model/ensembl_v103/tool_resources/capture_kits
reference_fasta: /home/tgenref/homo_sapiens/grch38_hg38/hg38_tempe/genome_reference/GRCh38tempe_decoy_alts_hla_masked.fa
reference_fasta_2bit: /home/tgenref/homo_sapiens/grch38_hg38/hg38_tempe/genome_reference/GRCh38tempe_decoy_alts_hla_masked.2bit
reference_fai: /home/tgenref/homo_sapiens/grch38_hg38/hg38_tempe/genome_reference/GRCh38tempe_decoy_alts_hla_masked.fa.fai
reference_dict: /home/tgenref/homo_sapiens/grch38_hg38/hg38_tempe/genome_reference/GRCh38tempe_decoy_alts_hla_masked.dict
reference_non_N_interval_list: /home/tgenref/homo_sapiens/grch38_hg38/hg38_tempe/tool_resources/samtools_stats/GRCh38tempe_decoy_alts_hla_masked_samstats_no_N_1based_primary_contigs_no_chrX_chrY.txt
dbsnp: /home/tgenref/homo_sapiens/grch38_hg38/public_databases/dbsnp/b154/dbSNP_b154_hg38tgen.bcf
gnomad_exome: /home/tgenref/homo_sapiens/grch38_hg38/public_databases/gnomad/r2.1.1/gnomad.exomes.r2.1.1.sites.liftover_grch38_AnnotationReference.bcf
gnomad_genome: /home/tgenref/homo_sapiens/grch38_hg38/public_databases/gnomad/r3.1.2/gnomad.genomes.r3.1.2.sites.pass.reduced.bcf
gnomad_exome_mutect_germlinereference: /home/tgenref/homo_sapiens/grch38_hg38/public_databases/gnomad/r2.1.1/gnomad.exomes.r2.1.1.sites.liftover_grch38_ForMutect.vcf.gz
gnomad_genome_mutect_germlinereference: /home/tgenref/homo_sapiens/grch38_hg38/public_databases/gnomad/r3.1.2/gnomad.genomes.r3.1.2.sites.pass.AnnotationReference.vcf.gz
gnomad_exome_mutect_contamination: /home/tgenref/homo_sapiens/grch38_hg38/public_databases/gnomad/r2.1.1/gnomad.exomes.r2.1.1.sites.liftover_grch38_ForMutectContamination.vcf.gz
gnomad_genome_mutect_contamination: /home/tgenref/homo_sapiens/grch38_hg38/public_databases/gnomad/r3.1.2/gnomad.genomes.r3.1.2.sites.pass.ForMutectContamination.vcf.gz
cosmic_coding: /home/tgenref/homo_sapiens/grch38_hg38/public_databases/cosmic/v96/CosmicCodingMuts_v96_hg38_tempe.bcf
cosmic_noncoding: /home/tgenref/homo_sapiens/grch38_hg38/public_databases/cosmic/v96/CosmicNonCodingMuts_v96_hg38_tempe.bcf
clinvar: /home/tgenref/homo_sapiens/grch38_hg38/public_databases/clinvar/20220910/clinvar_20220910_hg38_tempe.bcf
topmed: /home/tgenref/homo_sapiens/grch38_hg38/public_databases/topmed/freeze8/All.BRAVO_TOPMed_Freeze_8.bcf
bcftools_annotate_contig_update_ucsc2ensembl: /home/tgenref/homo_sapiens/grch38_hg38/hg38_tempe/tool_resources/bcftools/GRCh38_PrimaryContigs_UCSC_2_Ensembl_CrossMap.txt
denylist: /home/tgenref/homo_sapiens/grch38_hg38/public_databases/encode/Blacklist-2.0/lists/hg38-blacklist.v2.bed.gz
reference_msisensor_pro: /home/tgenref/homo_sapiens/grch38_hg38/hg38_tempe/tool_resources/msisensor_pro_v1.1.a/GRCh38tempe_decoy_alts_hla_masked.microsatellites.list
fish_probe_locations: /home/tgenref/homo_sapiens/grch38_hg38/hg38tgen/tool_resources/seq_fish/GRCh38_Myeloma_FISH_Probe_Locations_for_CNVear.bed
cnvear_locations: /home/tgenref/homo_sapiens/grch38_hg38/hg38_tempe/gene_model/ensembl_v103/Homo_sapiens.GRCh38.103.ucsc.cnvear.bed
required_scripts:
bpure: b_pure.py
manta_prepare_sv_vcf: manta_prepare_sv_vcf.py
pairoscope_mm_igtx_calling_script: mm_igtx_pairoscope_calling_b38.py
cna_seg_extend: seg_extend.py
plotCNVplus_Rscript: plotCNVplus.R
plotSamStats_Rscript: summarize_samstats.R
summarize_mm_igtx_Rscript: summarize_Ig.R
process_assembled_bam: Process_Assembled_BAM.py
stats2json: samStats2json.py
stats2lims: uploadStats2Lims.py
sigprofiler: sigprofiler.py
verifybamid_plot: verifybamid_plot.R
gatk_known_sites:
- /home/tgenref/homo_sapiens/grch38_hg38/public_databases/broad_resource_bundle/Homo_sapiens_assembly38.dbsnp138.vcf
- /home/tgenref/homo_sapiens/grch38_hg38/public_databases/broad_resource_bundle/Homo_sapiens_assembly38.known_indels.vcf.gz
- /home/tgenref/homo_sapiens/grch38_hg38/public_databases/broad_resource_bundle/Mills_and_1000G_gold_standard.indels.hg38.vcf.gz
gatk_cnn_resources:
- /home/tgenref/homo_sapiens/grch38_hg38/public_databases/broad_resource_bundle/hapmap_3.3.hg38.vcf.gz
- /home/tgenref/homo_sapiens/grch38_hg38/public_databases/broad_resource_bundle/Homo_sapiens_assembly38.known_indels.vcf.gz
- /home/tgenref/homo_sapiens/grch38_hg38/public_databases/broad_resource_bundle/Mills_and_1000G_gold_standard.indels.hg38.vcf.gz
bwa_index: /home/tgenref/homo_sapiens/grch38_hg38/hg38_tempe/tool_resources/bwa_0.7.17/GRCh38tempe_decoy_alts_hla_masked.fa
bwa_mem2_index: /home/tgenref/homo_sapiens/grch38_hg38/hg38_tempe/tool_resources/bwa_2.2.1/GRCh38tempe_decoy_alts_hla_masked.fa
gtf: /home/tgenref/homo_sapiens/grch38_hg38/hg38_tempe/gene_model/ensembl_v103/Homo_sapiens.GRCh38.103.ucsc.gtf
ref_flat: /home/tgenref/homo_sapiens/grch38_hg38/hg38_tempe/gene_model/ensembl_v103/Homo_sapiens.GRCh38.103.ucsc.refFlat.txt
ig_ENST_filter: /home/tgenref/homo_sapiens/grch38_hg38/hg38_tempe/gene_model/ensembl_v103/disease_specific_resources/myeloma/Homo_sapiens_GRCh38_103_ucsc_ig_ENST_to_filter_out.tsv
# igtx_regions: /home/tgenref/homo_sapiens/grch38_hg38/hg38_tempe/gene_model/ensembl_v103/disease_specific_resources/myeloma/Homo_sapiens_GRCh38_103_ucsc_igtx_regions.bed
igtx_regions:
- {"contig": "chr2", "start": 88750483, "stop": 90261139, "name": "IgK" }
- {"contig": "chr14", "start": 105533663, "stop": 106881350, "name": "IgH" }
- {"contig": "chr22", "start": 21995603, "stop": 23057822, "name": "IgL" }
# igtx_gene_regions: /home/tgenref/homo_sapiens/grch38_hg38/hg38_tempe/gene_model/ensembl_v103/disease_specific_resources/myeloma/Homo_sapiens_GRCh38_103_ucsc_igtx_gene_regions.bed
igtx_gene_regions:
- {"contig": "chr4", "start": 1798273, "stop": 1998273, "name": "NSD2"}
- {"contig": "chr6", "start": 41632262, "stop": 42332262, "name": "CCND3"}
- {"contig": "chr8", "start": 124987758, "stop": 129487754, "name": "MYC"}
- {"contig": "chr8", "start": 142918584, "stop": 143925832, "name": "MAFA"}
- {"contig": "chr11", "start": 68732532, "stop": 69685232, "name": "CCND1"}
- {"contig": "chr12", "start": 3690834, "stop": 4690834, "name": "CCND2"}
- {"contig": "chr16", "start": 78096103, "stop": 79950000, "name": "MAF"}
- {"contig": "chr20", "start": 39671358, "stop": 40971360, "name": "MAFB"}
igtx_loci_and_gene_regions:
- {"contig": "chr2", "start": 88750483, "stop": 90261139, "name": "IgK" }
- {"contig": "chr4", "start": 1798273, "stop": 1998273, "name": "NSD2"}
- {"contig": "chr6", "start": 41632262, "stop": 42332262, "name": "CCND3"}
- {"contig": "chr8", "start": 124987758, "stop": 129487754, "name": "MYC"}
- {"contig": "chr8", "start": 142918584, "stop": 143925832, "name": "MAFA"}
- {"contig": "chr11", "start": 68732532, "stop": 69685232, "name": "CCND1"}
- {"contig": "chr12", "start": 3690834, "stop": 4690834, "name": "CCND2"}
- {"contig": "chr14", "start": 105533663, "stop": 106881350, "name": "IgH" }
- {"contig": "chr16", "start": 78096103, "stop": 79950000, "name": "MAF"}
- {"contig": "chr20", "start": 39671358, "stop": 40971360, "name": "MAFB"}
- {"contig": "chr22", "start": 21995603, "stop": 23057822, "name": "IgL" }
ribo_locations: /home/tgenref/homo_sapiens/grch38_hg38/hg38_tempe/gene_model/ensembl_v103/Homo_sapiens.GRCh38.103.ucsc.ribo.interval_list
gatk_cnv_primary_contigs_female: /home/tgenref/homo_sapiens/grch38_hg38/hg38_tempe/tool_resources/gatk_cnv/Homo_sapiens.GRCh38.primary.contigs.female.interval_list
gatk_cnv_primary_contigs_male: /home/tgenref/homo_sapiens/grch38_hg38/hg38_tempe/tool_resources/gatk_cnv/Homo_sapiens.GRCh38.primary.contigs.male.interval_list
encode_denylist: /home/tgenref/homo_sapiens/grch38_hg38/public_databases/ncbi/Encode_deny_list_with_ncbi_centromere.merged.bed
centromere: /home/tgenref/homo_sapiens/grch38_hg38/public_databases/ncbi/Modeled_regions_for_GRCh38_centromere_blacklist_merged.bed
somatic_GRCh38_1000g_pon: /home/tgenref/homo_sapiens/grch38_hg38/public_databases/1000G/1000g_pon.hg38.vcf.gz
known_chip_snv: /home/tgenref/homo_sapiens/grch38_hg38/hg38_tempe/tool_resources/CHIP/known_chip_snv.vcf.gz
chip_genes_list: /home/tgenref/homo_sapiens/grch38_hg38/hg38_tempe/tool_resources/CHIP/chip_genes.bed
mappability_track: /home/tgenref/homo_sapiens/grch38_hg38/public_databases/bismap/k100.umap.no_header.bed
dj_window: /home/tgenref/homo_sapiens/grch38_hg38/hg38_tempe/tool_resources/bpure/dj_region_1kb_windowed.bed
salmon_index: /home/tgenref/homo_sapiens/grch38_hg38/hg38_tempe/gene_model/ensembl_v103/tool_resources/salmon_1.2.1-gompi-2019a/salmon_puff_75merPlus
sex_check_targets: /home/tgenref/homo_sapiens/grch38_hg38/hg38_tempe/tool_resources/tgen_gender_check/chrx_common_dbSNPv152_snv_exons.bed
sex_check_vcf: /home/tgenref/homo_sapiens/grch38_hg38/hg38_tempe/tool_resources/tgen_gender_check/chrx_common_dbSNPv152_snv_exons.vcf.gz
star_fasta: /home/tgenref/homo_sapiens/grch38_hg38/hg38_tempe/genome_reference/GRCh38tempe_decoy_masked.fa
star_indices_path: /home/tgenref/homo_sapiens/grch38_hg38/hg38_tempe/gene_model/ensembl_v103/tool_resources/star_2.7.5a
starfusion_index: /home/tgenref/homo_sapiens/grch38_hg38/hg38_tempe/gene_model/ensembl_v103/tool_resources/starFusion_gencode_v37/starFusion_Resources/ctat_genome_lib_build_dir
strandedness_options:
inward-unstranded-notapplicable:
salmon: "IU"
featurecounts: "0"
collectrnaseqmetrics: "NONE"
inward-stranded-forward:
salmon: "ISF"
featurecounts: "1"
collectrnaseqmetrics: "FIRST_READ_TRANSCRIPTION_STRAND"
inward-stranded-reverse:
salmon: "ISR"
featurecounts: "2"
collectrnaseqmetrics: "SECOND_READ_TRANSCRIPTION_STRAND"
umi_options:
correct_umi_umi_files: /home/tgenref/assay_files/twist_umi_adaptor_system/known_umi_sequences.txt
correct_umi_max_mismatches: 1
correct_umi_min_distance: 2
correct_umi_read_structure: "5M2S+T 5M2S+T"
group_reads_edits: 1
group_reads_min_map_q: 1
group_reads_strategy: "paired"
consensus_error_rate_pre_umi: 45
consensus_error_rate_post_umi: 40
consensus_min_input_base_quality: 10
filter_min_reads: 1
filter_min_base_quality: 30
filter_max_no_call_fraction: 0.1
filter_max_base_error_rate: 0.1
somatic_variant_filtering_options:
genome:
vcfmerger_exclude_filter: "(FMT/DP<10 | FMT/AR[0]>=0.02 | FMT/AR[1]<0.05)"
exome:
vcfmerger_exclude_filter: "(FMT/DP<10 | FMT/AR[0]>=0.02 | FMT/AR[1]<0.05)"
tumor_only_variant_filtering_options:
genome:
COSMIC_Ratio_Threshold: 0.10
vcfmerger_exclude_filter: "(FMT/DP<10 | FMT/AR[0]>=0.02 | FMT/AR[1]<0.05)"
exome:
COSMIC_Ratio_Threshold: 0.10
vcfmerger_exclude_filter: "(FMT/DP<10 | FMT/AR[0]>=0.02 | FMT/AR[1]<0.05)"
cnvear_copy_number_thresholds:
genome:
high_gain: 1.32
gain: 0.16
het_loss: -0.16
hom_loss: -1.32
exome:
high_gain: 1.32
gain: 0.16
het_loss: -0.16
hom_loss: -1.32
snpSniffer_sites: /home/tgenref/homo_sapiens/grch38_hg38/hg38_tempe/tool_resources/snpSniffer/positions_387_hg38_ucsc.txt
snpSniffer_database: /home/tgenref/homo_sapiens/grch38_hg38/hg38_tempe/tool_resources/snpSniffer/databaseV5_hg38_ucsc.ini
vep_data: /home/tgenref/homo_sapiens/grch38_hg38/tool_specific_resources/vep/v103/
vep_canonical_cds_intervals: /home/tgenref/homo_sapiens/grch38_hg38/hg38_tempe/gene_model/ensembl_v103/Homo_sapiens.GRCh38.103.ucsc.flt_canonical_vep.cds_padded.bed
verifybamid_resources: /home/tgenref/homo_sapiens/grch38_hg38/hg38_tempe/tool_resources/VerifyBamID_2.0.1
ns_effects:
- 'splice_acceptor_variant'
- 'splice_donor_variant'
- 'start_lost'
- 'exon_loss_variant'
- 'frameshift_variant'
- 'stop_gained'
- 'stop_lost'
- 'start_lost'
- 'rare_amino_acid_variant'
- 'missense_variant'
- 'inframe_insertion'
- 'disruptive_inframe_insertion'
- 'inframe_deletion'
- 'disruptive_inframe_deletion'
sequence_groupings:
# Sequence groupings for BQSR (same groups as found in the GATK WDL example).
- ['chr1']
- ['chr2']
- ['chr3']
- ['chr4']
- ['chr5']
- ['chr6']
- ['chr7']
- ['chr8']
- ['chr9']
- ['chr10']
- ['chr11']
- ['chr12', 'chr13']
- ['chr14', 'chr15']
- ['chr16', 'chr17']
- ['chr18', 'chr19', 'chr20']
- ['chr21', 'chr22']
- ['chrX', 'chrY', 'chrM', 'chr1_KI270706v1_random', 'chr1_KI270707v1_random', 'chr1_KI270708v1_random', 'chr1_KI270709v1_random', 'chr1_KI270710v1_random', 'chr1_KI270711v1_random', 'chr1_KI270712v1_random', 'chr1_KI270713v1_random', 'chr1_KI270714v1_random', 'chr2_KI270715v1_random', 'chr2_KI270716v1_random', 'chr3_GL000221v1_random', 'chr4_GL000008v2_random', 'chr5_GL000208v1_random', 'chr9_KI270717v1_random', 'chr9_KI270718v1_random', 'chr9_KI270719v1_random', 'chr9_KI270720v1_random', 'chr11_KI270721v1_random', 'chr14_GL000009v2_random', 'chr14_GL000225v1_random', 'chr14_KI270722v1_random', 'chr14_GL000194v1_random', 'chr14_KI270723v1_random', 'chr14_KI270724v1_random', 'chr14_KI270725v1_random', 'chr14_KI270726v1_random', 'chr15_KI270727v1_random', 'chr16_KI270728v1_random', 'chr17_GL000205v2_random', 'chr17_KI270729v1_random', 'chr17_KI270730v1_random', 'chr22_KI270731v1_random', 'chr22_KI270732v1_random', 'chr22_KI270733v1_random', 'chr22_KI270734v1_random', 'chr22_KI270735v1_random', 'chr22_KI270736v1_random', 'chr22_KI270737v1_random', 'chr22_KI270738v1_random', 'chr22_KI270739v1_random', 'chrY_KI270740v1_random', 'chrUn_KI270302v1', 'chrUn_KI270304v1', 'chrUn_KI270303v1', 'chrUn_KI270305v1', 'chrUn_KI270322v1', 'chrUn_KI270320v1', 'chrUn_KI270310v1', 'chrUn_KI270316v1', 'chrUn_KI270315v1', 'chrUn_KI270312v1', 'chrUn_KI270311v1', 'chrUn_KI270317v1', 'chrUn_KI270412v1', 'chrUn_KI270411v1', 'chrUn_KI270414v1', 'chrUn_KI270419v1', 'chrUn_KI270418v1', 'chrUn_KI270420v1', 'chrUn_KI270424v1', 'chrUn_KI270417v1', 'chrUn_KI270422v1', 'chrUn_KI270423v1', 'chrUn_KI270425v1', 'chrUn_KI270429v1', 'chrUn_KI270442v1', 'chrUn_KI270466v1', 'chrUn_KI270465v1', 'chrUn_KI270467v1', 'chrUn_KI270435v1', 'chrUn_KI270438v1', 'chrUn_KI270468v1', 'chrUn_KI270510v1', 'chrUn_KI270509v1', 'chrUn_KI270518v1', 'chrUn_KI270508v1', 'chrUn_KI270516v1', 'chrUn_KI270512v1', 'chrUn_KI270519v1', 'chrUn_KI270522v1', 'chrUn_KI270511v1', 'chrUn_KI270515v1', 'chrUn_KI270507v1', 'chrUn_KI270517v1', 'chrUn_KI270529v1', 'chrUn_KI270528v1', 'chrUn_KI270530v1', 'chrUn_KI270539v1', 'chrUn_KI270538v1', 'chrUn_KI270544v1', 'chrUn_KI270548v1', 'chrUn_KI270583v1', 'chrUn_KI270587v1', 'chrUn_KI270580v1', 'chrUn_KI270581v1', 'chrUn_KI270579v1', 'chrUn_KI270589v1', 'chrUn_KI270590v1', 'chrUn_KI270584v1', 'chrUn_KI270582v1', 'chrUn_KI270588v1', 'chrUn_KI270593v1', 'chrUn_KI270591v1', 'chrUn_KI270330v1', 'chrUn_KI270329v1', 'chrUn_KI270334v1', 'chrUn_KI270333v1', 'chrUn_KI270335v1', 'chrUn_KI270338v1', 'chrUn_KI270340v1', 'chrUn_KI270336v1', 'chrUn_KI270337v1', 'chrUn_KI270363v1', 'chrUn_KI270364v1', 'chrUn_KI270362v1', 'chrUn_KI270366v1', 'chrUn_KI270378v1', 'chrUn_KI270379v1', 'chrUn_KI270389v1', 'chrUn_KI270390v1', 'chrUn_KI270387v1', 'chrUn_KI270395v1', 'chrUn_KI270396v1', 'chrUn_KI270388v1', 'chrUn_KI270394v1', 'chrUn_KI270386v1', 'chrUn_KI270391v1', 'chrUn_KI270383v1', 'chrUn_KI270393v1', 'chrUn_KI270384v1', 'chrUn_KI270392v1', 'chrUn_KI270381v1', 'chrUn_KI270385v1', 'chrUn_KI270382v1', 'chrUn_KI270376v1', 'chrUn_KI270374v1', 'chrUn_KI270372v1', 'chrUn_KI270373v1', 'chrUn_KI270375v1', 'chrUn_KI270371v1', 'chrUn_KI270448v1', 'chrUn_KI270521v1', 'chrUn_GL000195v1', 'chrUn_GL000219v1', 'chrUn_GL000220v1', 'chrUn_GL000224v1', 'chrUn_KI270741v1', 'chrUn_GL000226v1', 'chrUn_GL000213v1', 'chrUn_KI270743v1', 'chrUn_KI270744v1', 'chrUn_KI270745v1', 'chrUn_KI270746v1', 'chrUn_KI270747v1', 'chrUn_KI270748v1', 'chrUn_KI270749v1', 'chrUn_KI270750v1', 'chrUn_KI270751v1', 'chrUn_KI270752v1', 'chrUn_KI270753v1', 'chrUn_KI270754v1', 'chrUn_KI270755v1', 'chrUn_KI270756v1', 'chrUn_KI270757v1', 'chrUn_GL000214v1', 'chrUn_KI270742v1', 'chrUn_GL000216v2', 'chrUn_GL000218v1', 'chr1_KI270762v1_alt', 'chr1_KI270766v1_alt', 'chr1_KI270760v1_alt', 'chr1_KI270765v1_alt', 'chr1_GL383518v1_alt', 'chr1_GL383519v1_alt', 'chr1_GL383520v2_alt', 'chr1_KI270764v1_alt', 'chr1_KI270763v1_alt', 'chr1_KI270759v1_alt', 'chr1_KI270761v1_alt', 'chr2_KI270770v1_alt', 'chr2_KI270773v1_alt', 'chr2_KI270774v1_alt', 'chr2_KI270769v1_alt', 'chr2_GL383521v1_alt', 'chr2_KI270772v1_alt', 'chr2_KI270775v1_alt', 'chr2_KI270771v1_alt', 'chr2_KI270768v1_alt', 'chr2_GL582966v2_alt', 'chr2_GL383522v1_alt', 'chr2_KI270776v1_alt', 'chr2_KI270767v1_alt', 'chr3_JH636055v2_alt', 'chr3_KI270783v1_alt', 'chr3_KI270780v1_alt', 'chr3_GL383526v1_alt', 'chr3_KI270777v1_alt', 'chr3_KI270778v1_alt', 'chr3_KI270781v1_alt', 'chr3_KI270779v1_alt', 'chr3_KI270782v1_alt', 'chr3_KI270784v1_alt', 'chr4_KI270790v1_alt', 'chr4_GL383528v1_alt', 'chr4_KI270787v1_alt', 'chr4_GL000257v2_alt', 'chr4_KI270788v1_alt', 'chr4_GL383527v1_alt', 'chr4_KI270785v1_alt', 'chr4_KI270789v1_alt', 'chr4_KI270786v1_alt', 'chr5_KI270793v1_alt', 'chr5_KI270792v1_alt', 'chr5_KI270791v1_alt', 'chr5_GL383532v1_alt', 'chr5_GL949742v1_alt', 'chr5_KI270794v1_alt', 'chr5_GL339449v2_alt', 'chr5_GL383530v1_alt', 'chr5_KI270796v1_alt', 'chr5_GL383531v1_alt', 'chr5_KI270795v1_alt', 'chr6_GL000250v2_alt', 'chr6_KI270800v1_alt', 'chr6_KI270799v1_alt', 'chr6_GL383533v1_alt', 'chr6_KI270801v1_alt', 'chr6_KI270802v1_alt', 'chr6_KB021644v2_alt', 'chr6_KI270797v1_alt', 'chr6_KI270798v1_alt', 'chr7_KI270804v1_alt', 'chr7_KI270809v1_alt', 'chr7_KI270806v1_alt', 'chr7_GL383534v2_alt', 'chr7_KI270803v1_alt', 'chr7_KI270808v1_alt', 'chr7_KI270807v1_alt', 'chr7_KI270805v1_alt', 'chr8_KI270818v1_alt', 'chr8_KI270812v1_alt', 'chr8_KI270811v1_alt', 'chr8_KI270821v1_alt', 'chr8_KI270813v1_alt', 'chr8_KI270822v1_alt', 'chr8_KI270814v1_alt',]
- ['chr8_KI270810v1_alt', 'chr8_KI270819v1_alt', 'chr8_KI270820v1_alt', 'chr8_KI270817v1_alt', 'chr8_KI270816v1_alt', 'chr8_KI270815v1_alt', 'chr9_GL383539v1_alt', 'chr9_GL383540v1_alt', 'chr9_GL383541v1_alt', 'chr9_GL383542v1_alt', 'chr9_KI270823v1_alt', 'chr10_GL383545v1_alt', 'chr10_KI270824v1_alt', 'chr10_GL383546v1_alt', 'chr10_KI270825v1_alt', 'chr11_KI270832v1_alt', 'chr11_KI270830v1_alt', 'chr11_KI270831v1_alt', 'chr11_KI270829v1_alt', 'chr11_GL383547v1_alt', 'chr11_JH159136v1_alt', 'chr11_JH159137v1_alt', 'chr11_KI270827v1_alt', 'chr11_KI270826v1_alt', 'chr12_GL877875v1_alt', 'chr12_GL877876v1_alt', 'chr12_KI270837v1_alt', 'chr12_GL383549v1_alt', 'chr12_KI270835v1_alt', 'chr12_GL383550v2_alt', 'chr12_GL383552v1_alt', 'chr12_GL383553v2_alt', 'chr12_KI270834v1_alt', 'chr12_GL383551v1_alt', 'chr12_KI270833v1_alt', 'chr12_KI270836v1_alt', 'chr13_KI270840v1_alt', 'chr13_KI270839v1_alt', 'chr13_KI270843v1_alt', 'chr13_KI270841v1_alt', 'chr13_KI270838v1_alt', 'chr13_KI270842v1_alt', 'chr14_KI270844v1_alt', 'chr14_KI270847v1_alt', 'chr14_KI270845v1_alt', 'chr14_KI270846v1_alt', 'chr15_KI270852v1_alt', 'chr15_KI270851v1_alt', 'chr15_KI270848v1_alt', 'chr15_GL383554v1_alt', 'chr15_KI270849v1_alt', 'chr15_GL383555v2_alt', 'chr15_KI270850v1_alt', 'chr16_KI270854v1_alt', 'chr16_KI270856v1_alt', 'chr16_KI270855v1_alt', 'chr16_KI270853v1_alt', 'chr16_GL383556v1_alt', 'chr16_GL383557v1_alt', 'chr17_GL383563v3_alt', 'chr17_KI270862v1_alt', 'chr17_KI270861v1_alt', 'chr17_KI270857v1_alt', 'chr17_JH159146v1_alt', 'chr17_JH159147v1_alt', 'chr17_GL383564v2_alt', 'chr17_GL000258v2_alt', 'chr17_GL383565v1_alt', 'chr17_KI270858v1_alt', 'chr17_KI270859v1_alt', 'chr17_GL383566v1_alt', 'chr17_KI270860v1_alt', 'chr18_KI270864v1_alt', 'chr18_GL383567v1_alt', 'chr18_GL383570v1_alt', 'chr18_GL383571v1_alt', 'chr18_GL383568v1_alt', 'chr18_GL383569v1_alt', 'chr18_GL383572v1_alt', 'chr18_KI270863v1_alt', 'chr19_KI270868v1_alt', 'chr19_KI270865v1_alt', 'chr19_GL383573v1_alt', 'chr19_GL383575v2_alt', 'chr19_GL383576v1_alt', 'chr19_GL383574v1_alt', 'chr19_KI270866v1_alt', 'chr19_KI270867v1_alt', 'chr19_GL949746v1_alt', 'chr20_GL383577v2_alt', 'chr20_KI270869v1_alt', 'chr20_KI270871v1_alt', 'chr20_KI270870v1_alt', 'chr21_GL383578v2_alt', 'chr21_KI270874v1_alt', 'chr21_KI270873v1_alt', 'chr21_GL383579v2_alt', 'chr21_GL383580v2_alt', 'chr21_GL383581v2_alt', 'chr21_KI270872v1_alt', 'chr22_KI270875v1_alt', 'chr22_KI270878v1_alt', 'chr22_KI270879v1_alt', 'chr22_KI270876v1_alt', 'chr22_KI270877v1_alt', 'chr22_GL383583v2_alt', 'chr22_GL383582v2_alt', 'chrX_KI270880v1_alt', 'chrX_KI270881v1_alt', 'chr19_KI270882v1_alt', 'chr19_KI270883v1_alt', 'chr19_KI270884v1_alt', 'chr19_KI270885v1_alt', 'chr19_KI270886v1_alt', 'chr19_KI270887v1_alt', 'chr19_KI270888v1_alt', 'chr19_KI270889v1_alt', 'chr19_KI270890v1_alt', 'chr19_KI270891v1_alt', 'chr1_KI270892v1_alt', 'chr2_KI270894v1_alt', 'chr2_KI270893v1_alt', 'chr3_KI270895v1_alt', 'chr4_KI270896v1_alt', 'chr5_KI270897v1_alt', 'chr5_KI270898v1_alt', 'chr6_GL000251v2_alt', 'chr7_KI270899v1_alt', 'chr8_KI270901v1_alt', 'chr8_KI270900v1_alt', 'chr11_KI270902v1_alt', 'chr11_KI270903v1_alt', 'chr12_KI270904v1_alt', 'chr15_KI270906v1_alt', 'chr15_KI270905v1_alt', 'chr17_KI270907v1_alt', 'chr17_KI270910v1_alt', 'chr17_KI270909v1_alt', 'chr17_JH159148v1_alt', 'chr17_KI270908v1_alt', 'chr18_KI270912v1_alt', 'chr18_KI270911v1_alt', 'chr19_GL949747v2_alt', 'chr22_KB663609v1_alt', 'chrX_KI270913v1_alt', 'chr19_KI270914v1_alt', 'chr19_KI270915v1_alt', 'chr19_KI270916v1_alt', 'chr19_KI270917v1_alt', 'chr19_KI270918v1_alt', 'chr19_KI270919v1_alt', 'chr19_KI270920v1_alt', 'chr19_KI270921v1_alt', 'chr19_KI270922v1_alt', 'chr19_KI270923v1_alt', 'chr3_KI270924v1_alt', 'chr4_KI270925v1_alt', 'chr6_GL000252v2_alt', 'chr8_KI270926v1_alt', 'chr11_KI270927v1_alt', 'chr19_GL949748v2_alt', 'chr22_KI270928v1_alt', 'chr19_KI270929v1_alt', 'chr19_KI270930v1_alt', 'chr19_KI270931v1_alt', 'chr19_KI270932v1_alt', 'chr19_KI270933v1_alt', 'chr19_GL000209v2_alt', 'chr3_KI270934v1_alt', 'chr6_GL000253v2_alt', 'chr19_GL949749v2_alt', 'chr3_KI270935v1_alt', 'chr6_GL000254v2_alt', 'chr19_GL949750v2_alt', 'chr3_KI270936v1_alt', 'chr6_GL000255v2_alt', 'chr19_GL949751v2_alt', 'chr3_KI270937v1_alt', 'chr6_GL000256v2_alt', 'chr19_GL949752v1_alt', 'chr6_KI270758v1_alt', 'chr19_GL949753v2_alt', 'chr19_KI270938v1_alt', 'chrEBV', 'chrUn_KN707606v1_decoy', 'chrUn_KN707607v1_decoy', 'chrUn_KN707608v1_decoy', 'chrUn_KN707609v1_decoy', 'chrUn_KN707610v1_decoy', 'chrUn_KN707611v1_decoy', 'chrUn_KN707612v1_decoy', 'chrUn_KN707613v1_decoy', 'chrUn_KN707614v1_decoy', 'chrUn_KN707615v1_decoy', 'chrUn_KN707616v1_decoy', 'chrUn_KN707617v1_decoy', 'chrUn_KN707618v1_decoy', 'chrUn_KN707619v1_decoy', 'chrUn_KN707620v1_decoy', 'chrUn_KN707621v1_decoy', 'chrUn_KN707622v1_decoy', 'chrUn_KN707623v1_decoy', 'chrUn_KN707624v1_decoy', 'chrUn_KN707625v1_decoy', 'chrUn_KN707626v1_decoy', 'chrUn_KN707627v1_decoy', 'chrUn_KN707628v1_decoy', 'chrUn_KN707629v1_decoy', 'chrUn_KN707630v1_decoy', 'chrUn_KN707631v1_decoy', 'chrUn_KN707632v1_decoy', 'chrUn_KN707633v1_decoy', 'chrUn_KN707634v1_decoy', 'chrUn_KN707635v1_decoy', 'chrUn_KN707636v1_decoy', 'chrUn_KN707637v1_decoy', 'chrUn_KN707638v1_decoy', 'chrUn_KN707639v1_decoy', 'chrUn_KN707640v1_decoy', 'chrUn_KN707641v1_decoy', 'chrUn_KN707642v1_decoy', 'chrUn_KN707643v1_decoy', 'chrUn_KN707644v1_decoy', 'chrUn_KN707645v1_decoy', 'chrUn_KN707646v1_decoy', 'chrUn_KN707647v1_decoy', 'chrUn_KN707648v1_decoy', 'chrUn_KN707649v1_decoy', 'chrUn_KN707650v1_decoy', 'chrUn_KN707651v1_decoy', 'chrUn_KN707652v1_decoy', 'chrUn_KN707653v1_decoy', 'chrUn_KN707654v1_decoy', 'chrUn_KN707655v1_decoy', 'chrUn_KN707656v1_decoy', 'chrUn_KN707657v1_decoy', 'chrUn_KN707658v1_decoy', 'chrUn_KN707659v1_decoy', 'chrUn_KN707660v1_decoy', 'chrUn_KN707661v1_decoy', 'chrUn_KN707662v1_decoy', 'chrUn_KN707663v1_decoy', 'chrUn_KN707664v1_decoy', 'chrUn_KN707665v1_decoy', 'chrUn_KN707666v1_decoy', 'chrUn_KN707667v1_decoy', 'chrUn_KN707668v1_decoy', 'chrUn_KN707669v1_decoy', 'chrUn_KN707670v1_decoy', 'chrUn_KN707671v1_decoy', 'chrUn_KN707672v1_decoy', 'chrUn_KN707673v1_decoy', 'chrUn_KN707674v1_decoy', 'chrUn_KN707675v1_decoy', 'chrUn_KN707676v1_decoy', 'chrUn_KN707677v1_decoy', 'chrUn_KN707678v1_decoy', 'chrUn_KN707679v1_decoy', 'chrUn_KN707680v1_decoy', 'chrUn_KN707681v1_decoy', 'chrUn_KN707682v1_decoy', 'chrUn_KN707683v1_decoy', 'chrUn_KN707684v1_decoy', 'chrUn_KN707685v1_decoy', 'chrUn_KN707686v1_decoy', 'chrUn_KN707687v1_decoy', 'chrUn_KN707688v1_decoy', 'chrUn_KN707689v1_decoy', 'chrUn_KN707690v1_decoy', 'chrUn_KN707691v1_decoy', 'chrUn_KN707692v1_decoy', 'chrUn_KN707693v1_decoy', 'chrUn_KN707694v1_decoy', 'chrUn_KN707695v1_decoy', 'chrUn_KN707696v1_decoy', 'chrUn_KN707697v1_decoy', 'chrUn_KN707698v1_decoy', 'chrUn_KN707699v1_decoy', 'chrUn_KN707700v1_decoy', 'chrUn_KN707701v1_decoy', 'chrUn_KN707702v1_decoy', 'chrUn_KN707703v1_decoy', 'chrUn_KN707704v1_decoy', 'chrUn_KN707705v1_decoy', 'chrUn_KN707706v1_decoy', 'chrUn_KN707707v1_decoy', 'chrUn_KN707708v1_decoy', 'chrUn_KN707709v1_decoy', 'chrUn_KN707710v1_decoy', 'chrUn_KN707711v1_decoy', 'chrUn_KN707712v1_decoy', 'chrUn_KN707713v1_decoy', 'chrUn_KN707714v1_decoy', 'chrUn_KN707715v1_decoy', 'chrUn_KN707716v1_decoy', 'chrUn_KN707717v1_decoy', 'chrUn_KN707718v1_decoy', 'chrUn_KN707719v1_decoy', 'chrUn_KN707720v1_decoy', 'chrUn_KN707721v1_decoy', 'chrUn_KN707722v1_decoy', 'chrUn_KN707723v1_decoy', 'chrUn_KN707724v1_decoy', 'chrUn_KN707725v1_decoy', 'chrUn_KN707726v1_decoy', 'chrUn_KN707727v1_decoy', 'chrUn_KN707728v1_decoy', 'chrUn_KN707729v1_decoy', 'chrUn_KN707730v1_decoy', 'chrUn_KN707731v1_decoy', 'chrUn_KN707732v1_decoy', 'chrUn_KN707733v1_decoy', 'chrUn_KN707734v1_decoy', 'chrUn_KN707735v1_decoy', 'chrUn_KN707736v1_decoy', 'chrUn_KN707737v1_decoy', 'chrUn_KN707738v1_decoy', 'chrUn_KN707739v1_decoy', 'chrUn_KN707740v1_decoy', 'chrUn_KN707741v1_decoy', 'chrUn_KN707742v1_decoy', 'chrUn_KN707743v1_decoy', 'chrUn_KN707744v1_decoy', 'chrUn_KN707745v1_decoy', 'chrUn_KN707746v1_decoy', 'chrUn_KN707747v1_decoy', 'chrUn_KN707748v1_decoy', 'chrUn_KN707749v1_decoy', 'chrUn_KN707750v1_decoy', 'chrUn_KN707751v1_decoy', 'chrUn_KN707752v1_decoy', 'chrUn_KN707753v1_decoy', 'chrUn_KN707754v1_decoy', 'chrUn_KN707755v1_decoy', 'chrUn_KN707756v1_decoy', 'chrUn_KN707757v1_decoy', 'chrUn_KN707758v1_decoy', 'chrUn_KN707759v1_decoy', 'chrUn_KN707760v1_decoy', 'chrUn_KN707761v1_decoy', 'chrUn_KN707762v1_decoy', 'chrUn_KN707763v1_decoy', 'chrUn_KN707764v1_decoy', 'chrUn_KN707765v1_decoy', 'chrUn_KN707766v1_decoy', 'chrUn_KN707767v1_decoy', 'chrUn_KN707768v1_decoy', 'chrUn_KN707769v1_decoy', 'chrUn_KN707770v1_decoy', 'chrUn_KN707771v1_decoy', 'chrUn_KN707772v1_decoy', 'chrUn_KN707773v1_decoy', 'chrUn_KN707774v1_decoy', 'chrUn_KN707775v1_decoy', 'chrUn_KN707776v1_decoy', 'chrUn_KN707777v1_decoy', 'chrUn_KN707778v1_decoy', 'chrUn_KN707779v1_decoy', 'chrUn_KN707780v1_decoy', 'chrUn_KN707781v1_decoy', 'chrUn_KN707782v1_decoy', 'chrUn_KN707783v1_decoy', 'chrUn_KN707784v1_decoy', 'chrUn_KN707785v1_decoy', 'chrUn_KN707786v1_decoy', 'chrUn_KN707787v1_decoy', 'chrUn_KN707788v1_decoy', 'chrUn_KN707789v1_decoy', 'chrUn_KN707790v1_decoy', 'chrUn_KN707791v1_decoy', 'chrUn_KN707792v1_decoy', 'chrUn_KN707793v1_decoy', 'chrUn_KN707794v1_decoy', 'chrUn_KN707795v1_decoy', 'chrUn_KN707796v1_decoy', 'chrUn_KN707797v1_decoy', 'chrUn_KN707798v1_decoy', 'chrUn_KN707799v1_decoy', 'chrUn_KN707800v1_decoy', 'chrUn_KN707801v1_decoy', 'chrUn_KN707802v1_decoy', 'chrUn_KN707803v1_decoy', 'chrUn_KN707804v1_decoy', 'chrUn_KN707805v1_decoy', 'chrUn_KN707806v1_decoy', 'chrUn_KN707807v1_decoy', 'chrUn_KN707808v1_decoy', 'chrUn_KN707809v1_decoy', 'chrUn_KN707810v1_decoy', 'chrUn_KN707811v1_decoy', 'chrUn_KN707812v1_decoy', 'chrUn_KN707813v1_decoy', 'chrUn_KN707814v1_decoy', 'chrUn_KN707815v1_decoy', 'chrUn_KN707816v1_decoy', 'chrUn_KN707817v1_decoy', 'chrUn_KN707818v1_decoy', 'chrUn_KN707819v1_decoy', 'chrUn_KN707820v1_decoy', 'chrUn_KN707821v1_decoy', 'chrUn_KN707822v1_decoy', 'chrUn_KN707823v1_decoy', 'chrUn_KN707824v1_decoy', 'chrUn_KN707825v1_decoy', 'chrUn_KN707826v1_decoy', 'chrUn_KN707827v1_decoy', 'chrUn_KN707828v1_decoy', 'chrUn_KN707829v1_decoy', 'chrUn_KN707830v1_decoy', 'chrUn_KN707831v1_decoy', 'chrUn_KN707832v1_decoy', 'chrUn_KN707833v1_decoy', 'chrUn_KN707834v1_decoy', 'chrUn_KN707835v1_decoy', 'chrUn_KN707836v1_decoy', 'chrUn_KN707837v1_decoy', 'chrUn_KN707838v1_decoy', 'chrUn_KN707839v1_decoy', 'chrUn_KN707840v1_decoy', 'chrUn_KN707841v1_decoy', 'chrUn_KN707842v1_decoy', 'chrUn_KN707843v1_decoy', 'chrUn_KN707844v1_decoy', 'chrUn_KN707845v1_decoy', 'chrUn_KN707846v1_decoy', 'chrUn_KN707847v1_decoy', 'chrUn_KN707848v1_decoy', 'chrUn_KN707849v1_decoy', 'chrUn_KN707850v1_decoy', 'chrUn_KN707851v1_decoy', 'chrUn_KN707852v1_decoy', 'chrUn_KN707853v1_decoy', 'chrUn_KN707854v1_decoy', 'chrUn_KN707855v1_decoy', 'chrUn_KN707856v1_decoy', 'chrUn_KN707857v1_decoy', 'chrUn_KN707858v1_decoy', 'chrUn_KN707859v1_decoy', 'chrUn_KN707860v1_decoy', 'chrUn_KN707861v1_decoy', 'chrUn_KN707862v1_decoy', 'chrUn_KN707863v1_decoy', 'chrUn_KN707864v1_decoy', 'chrUn_KN707865v1_decoy', 'chrUn_KN707866v1_decoy', 'chrUn_KN707867v1_decoy', 'chrUn_KN707868v1_decoy', 'chrUn_KN707869v1_decoy', 'chrUn_KN707870v1_decoy', 'chrUn_KN707871v1_decoy', 'chrUn_KN707872v1_decoy', 'chrUn_KN707873v1_decoy', 'chrUn_KN707874v1_decoy', 'chrUn_KN707875v1_decoy', 'chrUn_KN707876v1_decoy', 'chrUn_KN707877v1_decoy', 'chrUn_KN707878v1_decoy', 'chrUn_KN707879v1_decoy', 'chrUn_KN707880v1_decoy', 'chrUn_KN707881v1_decoy', 'chrUn_KN707882v1_decoy', 'chrUn_KN707883v1_decoy', 'chrUn_KN707884v1_decoy', 'chrUn_KN707885v1_decoy', 'chrUn_KN707886v1_decoy', 'chrUn_KN707887v1_decoy', 'chrUn_KN707888v1_decoy', 'chrUn_KN707889v1_decoy', 'chrUn_KN707890v1_decoy', 'chrUn_KN707891v1_decoy', 'chrUn_KN707892v1_decoy', 'chrUn_KN707893v1_decoy', 'chrUn_KN707894v1_decoy', 'chrUn_KN707895v1_decoy', 'chrUn_KN707896v1_decoy', 'chrUn_KN707897v1_decoy', 'chrUn_KN707898v1_decoy', 'chrUn_KN707899v1_decoy', 'chrUn_KN707900v1_decoy', 'chrUn_KN707901v1_decoy', 'chrUn_KN707902v1_decoy', 'chrUn_KN707903v1_decoy', 'chrUn_KN707904v1_decoy', 'chrUn_KN707905v1_decoy', 'chrUn_KN707906v1_decoy', 'chrUn_KN707907v1_decoy', 'chrUn_KN707908v1_decoy', 'chrUn_KN707909v1_decoy', 'chrUn_KN707910v1_decoy', 'chrUn_KN707911v1_decoy', 'chrUn_KN707912v1_decoy', 'chrUn_KN707913v1_decoy', 'chrUn_KN707914v1_decoy', 'chrUn_KN707915v1_decoy', 'chrUn_KN707916v1_decoy', 'chrUn_KN707917v1_decoy', 'chrUn_KN707918v1_decoy', 'chrUn_KN707919v1_decoy', 'chrUn_KN707920v1_decoy', 'chrUn_KN707921v1_decoy', 'chrUn_KN707922v1_decoy', 'chrUn_KN707923v1_decoy', 'chrUn_KN707924v1_decoy', 'chrUn_KN707925v1_decoy', 'chrUn_KN707926v1_decoy', 'chrUn_KN707927v1_decoy', 'chrUn_KN707928v1_decoy', 'chrUn_KN707929v1_decoy', 'chrUn_KN707930v1_decoy', 'chrUn_KN707931v1_decoy', 'chrUn_KN707932v1_decoy', 'chrUn_KN707933v1_decoy', 'chrUn_KN707934v1_decoy', 'chrUn_KN707935v1_decoy', 'chrUn_KN707936v1_decoy', 'chrUn_KN707937v1_decoy', 'chrUn_KN707938v1_decoy', 'chrUn_KN707939v1_decoy', 'chrUn_KN707940v1_decoy', 'chrUn_KN707941v1_decoy', 'chrUn_KN707942v1_decoy', 'chrUn_KN707943v1_decoy', 'chrUn_KN707944v1_decoy', 'chrUn_KN707945v1_decoy', 'chrUn_KN707946v1_decoy', 'chrUn_KN707947v1_decoy', 'chrUn_KN707948v1_decoy', 'chrUn_KN707949v1_decoy', 'chrUn_KN707950v1_decoy', 'chrUn_KN707951v1_decoy', 'chrUn_KN707952v1_decoy', 'chrUn_KN707953v1_decoy', 'chrUn_KN707954v1_decoy', 'chrUn_KN707955v1_decoy', 'chrUn_KN707956v1_decoy', 'chrUn_KN707957v1_decoy', 'chrUn_KN707958v1_decoy', 'chrUn_KN707959v1_decoy', 'chrUn_KN707960v1_decoy', 'chrUn_KN707961v1_decoy', 'chrUn_KN707962v1_decoy', 'chrUn_KN707963v1_decoy', 'chrUn_KN707964v1_decoy', 'chrUn_KN707965v1_decoy', 'chrUn_KN707966v1_decoy', 'chrUn_KN707967v1_decoy', 'chrUn_KN707968v1_decoy', 'chrUn_KN707969v1_decoy', 'chrUn_KN707970v1_decoy', 'chrUn_KN707971v1_decoy', 'chrUn_KN707972v1_decoy', 'chrUn_KN707973v1_decoy', 'chrUn_KN707974v1_decoy', 'chrUn_KN707975v1_decoy', 'chrUn_KN707976v1_decoy', 'chrUn_KN707977v1_decoy', 'chrUn_KN707978v1_decoy', 'chrUn_KN707979v1_decoy', 'chrUn_KN707980v1_decoy', 'chrUn_KN707981v1_decoy', 'chrUn_KN707982v1_decoy', 'chrUn_KN707983v1_decoy', 'chrUn_KN707984v1_decoy', 'chrUn_KN707985v1_decoy', 'chrUn_KN707986v1_decoy', 'chrUn_KN707987v1_decoy', 'chrUn_KN707988v1_decoy', 'chrUn_KN707989v1_decoy', 'chrUn_KN707990v1_decoy', 'chrUn_KN707991v1_decoy', 'chrUn_KN707992v1_decoy', 'chrUn_JTFH01000001v1_decoy', 'chrUn_JTFH01000002v1_decoy', 'chrUn_JTFH01000003v1_decoy', 'chrUn_JTFH01000004v1_decoy', 'chrUn_JTFH01000005v1_decoy', 'chrUn_JTFH01000006v1_decoy', 'chrUn_JTFH01000007v1_decoy', 'chrUn_JTFH01000008v1_decoy', 'chrUn_JTFH01000009v1_decoy', 'chrUn_JTFH01000010v1_decoy', 'chrUn_JTFH01000011v1_decoy', 'chrUn_JTFH01000012v1_decoy', 'chrUn_JTFH01000013v1_decoy', 'chrUn_JTFH01000014v1_decoy', 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'HLA-A*34:02:01', 'HLA-A*36:01', 'HLA-A*43:01', 'HLA-A*66:01:01', 'HLA-A*66:17', 'HLA-A*68:01:01:01', 'HLA-A*68:01:01:02', 'HLA-A*68:01:02:01', 'HLA-A*68:01:02:02', 'HLA-A*68:02:01:01', 'HLA-A*68:02:01:02', 'HLA-A*68:02:01:03', 'HLA-A*68:02:02', 'HLA-A*68:03:01', 'HLA-A*68:08:01', 'HLA-A*68:113', 'HLA-A*68:17', 'HLA-A*68:18N', 'HLA-A*68:22', 'HLA-A*68:71', 'HLA-A*69:01', 'HLA-A*74:01', 'HLA-A*74:02:01:01', 'HLA-A*74:02:01:02', 'HLA-A*80:01:01:01', 'HLA-A*80:01:01:02', 'HLA-B*07:02:01', 'HLA-B*07:05:01', 'HLA-B*07:06', 'HLA-B*07:156', 'HLA-B*07:33:01', 'HLA-B*07:41', 'HLA-B*07:44', 'HLA-B*07:50', 'HLA-B*08:01:01', 'HLA-B*08:08N', 'HLA-B*08:132', 'HLA-B*08:134', 'HLA-B*08:19N', 'HLA-B*08:20', 'HLA-B*08:33', 'HLA-B*08:79', 'HLA-B*13:01:01', 'HLA-B*13:02:01', 'HLA-B*13:02:03', 'HLA-B*13:02:09', 'HLA-B*13:08', 'HLA-B*13:15', 'HLA-B*13:25', 'HLA-B*14:01:01', 'HLA-B*14:02:01', 'HLA-B*14:07N', 'HLA-B*15:01:01:01', 'HLA-B*15:01:01:02N', 'HLA-B*15:01:01:03', 'HLA-B*15:02:01', 'HLA-B*15:03:01', 'HLA-B*15:04:01', 'HLA-B*15:07:01', 'HLA-B*15:108', 'HLA-B*15:10:01', 'HLA-B*15:11:01', 'HLA-B*15:13:01', 'HLA-B*15:16:01', 'HLA-B*15:17:01:01', 'HLA-B*15:17:01:02', 'HLA-B*15:18:01', 'HLA-B*15:220', 'HLA-B*15:25:01', 'HLA-B*15:27:01', 'HLA-B*15:32:01', 'HLA-B*15:42', 'HLA-B*15:58', 'HLA-B*15:66', 'HLA-B*15:77', 'HLA-B*15:83', 'HLA-B*18:01:01:01', 'HLA-B*18:01:01:02', 'HLA-B*18:02', 'HLA-B*18:03', 'HLA-B*18:17N', 'HLA-B*18:26', 'HLA-B*18:94N', 'HLA-B*27:04:01', 'HLA-B*27:05:02', 'HLA-B*27:05:18', 'HLA-B*27:06', 'HLA-B*27:07:01', 'HLA-B*27:131', 'HLA-B*27:24', 'HLA-B*27:25', 'HLA-B*27:32', 'HLA-B*35:01:01:01', 'HLA-B*35:01:01:02', 'HLA-B*35:01:22', 'HLA-B*35:02:01', 'HLA-B*35:03:01', 'HLA-B*35:05:01', 'HLA-B*35:08:01', 'HLA-B*35:14:02', 'HLA-B*35:241', 'HLA-B*35:41', 'HLA-B*37:01:01', 'HLA-B*37:01:05', 'HLA-B*38:01:01', 'HLA-B*38:02:01', 'HLA-B*38:14', 'HLA-B*39:01:01:01', 'HLA-B*39:01:01:02L', 'HLA-B*39:01:01:03', 'HLA-B*39:01:03', 'HLA-B*39:01:16', 'HLA-B*39:01:21', 'HLA-B*39:05:01', 'HLA-B*39:06:02', 'HLA-B*39:10:01', 'HLA-B*39:13:02', 'HLA-B*39:14', 'HLA-B*39:34', 'HLA-B*39:38Q', 'HLA-B*40:01:01', 'HLA-B*40:01:02', 'HLA-B*40:02:01', 'HLA-B*40:03', 'HLA-B*40:06:01:01', 'HLA-B*40:06:01:02', 'HLA-B*40:10:01', 'HLA-B*40:150', 'HLA-B*40:40', 'HLA-B*40:72:01', 'HLA-B*40:79', 'HLA-B*41:01:01', 'HLA-B*41:02:01', 'HLA-B*42:01:01', 'HLA-B*42:02', 'HLA-B*42:08', 'HLA-B*44:02:01:01', 'HLA-B*44:02:01:02S', 'HLA-B*44:02:01:03', 'HLA-B*44:02:17', 'HLA-B*44:02:27', 'HLA-B*44:03:01', 'HLA-B*44:03:02', 'HLA-B*44:04', 'HLA-B*44:09', 'HLA-B*44:138Q', 'HLA-B*44:150', 'HLA-B*44:23N', 'HLA-B*44:26', 'HLA-B*44:46', 'HLA-B*44:49', 'HLA-B*44:56N', 'HLA-B*45:01:01', 'HLA-B*45:04', 'HLA-B*46:01:01', 'HLA-B*46:01:05', 'HLA-B*47:01:01:01', 'HLA-B*47:01:01:02', 'HLA-B*48:01:01', 'HLA-B*48:03:01', 'HLA-B*48:04', 'HLA-B*48:08', 'HLA-B*49:01:01', 'HLA-B*49:32', 'HLA-B*50:01:01', 'HLA-B*51:01:01', 'HLA-B*51:01:02', 'HLA-B*51:02:01', 'HLA-B*51:07:01', 'HLA-B*51:42', 'HLA-B*52:01:01:01', 'HLA-B*52:01:01:02', 'HLA-B*52:01:01:03', 'HLA-B*52:01:02', 'HLA-B*53:01:01', 'HLA-B*53:11', 'HLA-B*54:01:01', 'HLA-B*54:18', 'HLA-B*55:01:01', 'HLA-B*55:01:03', 'HLA-B*55:02:01', 'HLA-B*55:12', 'HLA-B*55:24', 'HLA-B*55:48', 'HLA-B*56:01:01', 'HLA-B*56:03', 'HLA-B*56:04', 'HLA-B*57:01:01', 'HLA-B*57:03:01', 'HLA-B*57:06', 'HLA-B*57:11', 'HLA-B*57:29', 'HLA-B*58:01:01', 'HLA-B*58:31N', 'HLA-B*59:01:01:01', 'HLA-B*59:01:01:02', 'HLA-B*67:01:01', 'HLA-B*67:01:02', 'HLA-B*67:02', 'HLA-B*73:01', 'HLA-B*78:01:01', 'HLA-B*81:01', 'HLA-B*82:02:01', 'HLA-C*01:02:01', 'HLA-C*01:02:11', 'HLA-C*01:02:29', 'HLA-C*01:02:30', 'HLA-C*01:03', 'HLA-C*01:06', 'HLA-C*01:08', 'HLA-C*01:14', 'HLA-C*01:21', 'HLA-C*01:30', 'HLA-C*01:40', 'HLA-C*02:02:02:01', 'HLA-C*02:02:02:02', 'HLA-C*02:10', 'HLA-C*02:11', 'HLA-C*02:16:02', 'HLA-C*02:69', 'HLA-C*02:85', 'HLA-C*02:86', 'HLA-C*02:87', 'HLA-C*03:02:01', 'HLA-C*03:02:02:01', 'HLA-C*03:02:02:02', 'HLA-C*03:02:02:03', 'HLA-C*03:03:01', 'HLA-C*03:04:01:01', 'HLA-C*03:04:01:02', 'HLA-C*03:04:02', 'HLA-C*03:04:04', 'HLA-C*03:05', 'HLA-C*03:06', 'HLA-C*03:100', 'HLA-C*03:13:01', 'HLA-C*03:20N', 'HLA-C*03:219', 'HLA-C*03:261', 'HLA-C*03:40:01', 'HLA-C*03:41:02', 'HLA-C*03:46', 'HLA-C*03:61', 'HLA-C*04:01:01:01', 'HLA-C*04:01:01:02', 'HLA-C*04:01:01:03', 'HLA-C*04:01:01:04', 'HLA-C*04:01:01:05', 'HLA-C*04:01:62', 'HLA-C*04:03:01', 'HLA-C*04:06', 'HLA-C*04:09N', 'HLA-C*04:128', 'HLA-C*04:161', 'HLA-C*04:177', 'HLA-C*04:70', 'HLA-C*04:71', 'HLA-C*05:01:01:01', 'HLA-C*05:01:01:02', 'HLA-C*05:08', 'HLA-C*05:09:01', 'HLA-C*05:93', 'HLA-C*06:02:01:01', 'HLA-C*06:02:01:02', 'HLA-C*06:02:01:03', 'HLA-C*06:23', 'HLA-C*06:24', 'HLA-C*06:46N', 'HLA-C*07:01:01:01', 'HLA-C*07:01:01:02', 'HLA-C*07:01:02', 'HLA-C*07:01:19', 'HLA-C*07:01:27', 'HLA-C*07:01:45', 'HLA-C*07:02:01:01', 'HLA-C*07:02:01:02', 'HLA-C*07:02:01:03', 'HLA-C*07:02:01:04', 'HLA-C*07:02:01:05', 'HLA-C*07:02:05', 'HLA-C*07:02:06', 'HLA-C*07:02:64', 'HLA-C*07:04:01', 'HLA-C*07:04:02', 'HLA-C*07:06', 'HLA-C*07:149', 'HLA-C*07:18', 'HLA-C*07:19', 'HLA-C*07:26', 'HLA-C*07:30', 'HLA-C*07:32N', 'HLA-C*07:384', 'HLA-C*07:385', 'HLA-C*07:386', 'HLA-C*07:391', 'HLA-C*07:392', 'HLA-C*07:49', 'HLA-C*07:56:02', 'HLA-C*07:66', 'HLA-C*07:67', 'HLA-C*08:01:01', 'HLA-C*08:01:03', 'HLA-C*08:02:01:01', 'HLA-C*08:02:01:02', 'HLA-C*08:03:01', 'HLA-C*08:04:01', 'HLA-C*08:112', 'HLA-C*08:20', 'HLA-C*08:21', 'HLA-C*08:22', 'HLA-C*08:24', 'HLA-C*08:27', 'HLA-C*08:36N', 'HLA-C*08:40', 'HLA-C*08:41', 'HLA-C*08:62', 'HLA-C*12:02:02', 'HLA-C*12:03:01:01', 'HLA-C*12:03:01:02', 'HLA-C*12:08', 'HLA-C*12:13', 'HLA-C*12:19', 'HLA-C*12:22', 'HLA-C*12:99', 'HLA-C*14:02:01', 'HLA-C*14:03', 'HLA-C*14:21N', 'HLA-C*14:23', 'HLA-C*15:02:01', 'HLA-C*15:05:01', 'HLA-C*15:05:02', 'HLA-C*15:13', 'HLA-C*15:16', 'HLA-C*15:17', 'HLA-C*15:96Q', 'HLA-C*16:01:01', 'HLA-C*16:02:01', 'HLA-C*16:04:01', 'HLA-C*17:01:01:01', 'HLA-C*17:01:01:02', 'HLA-C*17:01:01:03', 'HLA-C*17:03', 'HLA-C*18:01', 'HLA-DQA1*01:01:02', 'HLA-DQA1*01:02:01:01', 'HLA-DQA1*01:02:01:02', 'HLA-DQA1*01:02:01:03', 'HLA-DQA1*01:02:01:04', 'HLA-DQA1*01:03:01:01', 'HLA-DQA1*01:03:01:02', 'HLA-DQA1*01:04:01:01', 'HLA-DQA1*01:04:01:02', 'HLA-DQA1*01:05:01', 'HLA-DQA1*01:07', 'HLA-DQA1*01:10', 'HLA-DQA1*01:11', 'HLA-DQA1*02:01', 'HLA-DQA1*03:01:01', 'HLA-DQA1*03:02', 'HLA-DQA1*03:03:01', 'HLA-DQA1*04:01:02:01', 'HLA-DQA1*04:01:02:02', 'HLA-DQA1*04:02', 'HLA-DQA1*05:01:01:01', 'HLA-DQA1*05:01:01:02', 'HLA-DQA1*05:03', 'HLA-DQA1*05:05:01:01', 'HLA-DQA1*05:05:01:02', 'HLA-DQA1*05:05:01:03', 'HLA-DQA1*05:11', 'HLA-DQA1*06:01:01', 'HLA-DQB1*02:01:01', 'HLA-DQB1*02:02:01', 'HLA-DQB1*03:01:01:01', 'HLA-DQB1*03:01:01:02', 'HLA-DQB1*03:01:01:03', 'HLA-DQB1*03:02:01', 'HLA-DQB1*03:03:02:01', 'HLA-DQB1*03:03:02:02', 'HLA-DQB1*03:03:02:03', 'HLA-DQB1*03:05:01', 'HLA-DQB1*05:01:01:01', 'HLA-DQB1*05:01:01:02', 'HLA-DQB1*05:03:01:01', 'HLA-DQB1*05:03:01:02', 'HLA-DQB1*06:01:01', 'HLA-DQB1*06:02:01', 'HLA-DQB1*06:03:01', 'HLA-DQB1*06:09:01', 'HLA-DRB1*01:01:01', 'HLA-DRB1*01:02:01', 'HLA-DRB1*03:01:01:01', 'HLA-DRB1*03:01:01:02', 'HLA-DRB1*04:03:01', 'HLA-DRB1*07:01:01:01', 'HLA-DRB1*07:01:01:02', 'HLA-DRB1*08:03:02', 'HLA-DRB1*09:21', 'HLA-DRB1*10:01:01', 'HLA-DRB1*11:01:01', 'HLA-DRB1*11:01:02', 'HLA-DRB1*11:04:01', 'HLA-DRB1*12:01:01', 'HLA-DRB1*12:17', 'HLA-DRB1*13:01:01', 'HLA-DRB1*13:02:01', 'HLA-DRB1*14:05:01', 'HLA-DRB1*14:54:01', 'HLA-DRB1*15:01:01:01', 'HLA-DRB1*15:01:01:02', 'HLA-DRB1*15:01:01:03', 'HLA-DRB1*15:01:01:04', 'HLA-DRB1*15:02:01', 'HLA-DRB1*15:03:01:01', 'HLA-DRB1*15:03:01:02', 'HLA-DRB1*16:02:01']
lims_contigs: "chr1,chr2,chr3,chr4,chr5,chr6,chr7,chr8,chr9,chr10,chr11,chr12,chr13,chr14,chr15,chr16,chr17,chr18,chr19,chr20,chr21,chr22,chrX,
chrY,
chrM,
chrUn_GL000220v1,
chr22_KI270733v1_random,
chrUn_KN707925v1_decoy,
chr14_KI270726v1_random,
chrUn_JTFH01000119v1_decoy,
chrUn_JTFH01000204v1_decoy,
chrUn_JTFH01000678v1_decoy,
chrUn_JTFH01000497v1_decoy,
chrUn_KN707927v1_decoy,
chrUn_JTFH01000562v1_decoy,
chrUn_JTFH01000659v1_decoy,
chrUn_JTFH01001134v1_decoy,
chrUn_JTFH01000888v1_decoy,
chrUn_JTFH01000695v1_decoy,
chrUn_JTFH01000697v1_decoy"
calling_contigs:
# Contigs in the genome build that should be considered for variant calling
# Note that chrM is not included in this list because the mitochrondria
# should be analyzed separately.
- {"contig": chr1, "length": 248956422}
- {"contig": chr2, "length": 242193529}
- {"contig": chr3, "length": 198295559}
- {"contig": chr4, "length": 190214555}
- {"contig": chr5, "length": 181538259}
- {"contig": chr6, "length": 170805979}
- {"contig": chr7, "length": 159345973}
- {"contig": chr8, "length": 145138636}
- {"contig": chr9, "length": 138394717}
- {"contig": chr10, "length": 133797422}
- {"contig": chr11, "length": 135086622}
- {"contig": chr12, "length": 133275309}
- {"contig": chr13, "length": 114364328}
- {"contig": chr14, "length": 107043718}
- {"contig": chr15, "length": 101991189}
- {"contig": chr16, "length": 90338345}
- {"contig": chr17, "length": 83257441}
- {"contig": chr18, "length": 80373285}
- {"contig": chr19, "length": 58617616}
- {"contig": chr20, "length": 64444167}
- {"contig": chr21, "length": 46709983}
- {"contig": chr22, "length": 50818468}
- {"contig": chrX, "length": 156040895}
- {"contig": chrY, "length": 57227415}
- {"contig": "chr1_KI270706v1_random", "length": 175055}
- {"contig": "chr1_KI270707v1_random", "length": 32032}
- {"contig": "chr1_KI270708v1_random", "length": 127682}
- {"contig": "chr1_KI270709v1_random", "length": 66860}
- {"contig": "chr1_KI270710v1_random", "length": 40176}
- {"contig": "chr1_KI270711v1_random", "length": 42210}
- {"contig": "chr1_KI270712v1_random", "length": 176043}
- {"contig": "chr1_KI270713v1_random", "length": 40745}
- {"contig": "chr1_KI270714v1_random", "length": 41717}
- {"contig": "chr2_KI270715v1_random", "length": 161471}
- {"contig": "chr2_KI270716v1_random", "length": 153799}
- {"contig": "chr3_GL000221v1_random", "length": 155397}
- {"contig": "chr4_GL000008v2_random", "length": 209709}
- {"contig": "chr5_GL000208v1_random", "length": 92689}
- {"contig": "chr9_KI270717v1_random", "length": 40062}
- {"contig": "chr9_KI270718v1_random", "length": 38054}
- {"contig": "chr9_KI270719v1_random", "length": 176845}
- {"contig": "chr9_KI270720v1_random", "length": 39050}
- {"contig": "chr11_KI270721v1_random", "length": 100316}
- {"contig": "chr14_GL000009v2_random", "length": 201709}
- {"contig": "chr14_GL000225v1_random", "length": 211173}
- {"contig": "chr14_KI270722v1_random", "length": 194050}
- {"contig": "chr14_GL000194v1_random", "length": 191469}
- {"contig": "chr14_KI270723v1_random", "length": 38115}
- {"contig": "chr14_KI270724v1_random", "length": 39555}
- {"contig": "chr14_KI270725v1_random", "length": 172810}
- {"contig": "chr14_KI270726v1_random", "length": 43739}
- {"contig": "chr15_KI270727v1_random", "length": 448248}
- {"contig": "chr16_KI270728v1_random", "length": 1872759}
- {"contig": "chr17_GL000205v2_random", "length": 185591}
- {"contig": "chr17_KI270729v1_random", "length": 280839}
- {"contig": "chr17_KI270730v1_random", "length": 112551}
- {"contig": "chr22_KI270731v1_random", "length": 150754}
- {"contig": "chr22_KI270732v1_random", "length": 41543}
- {"contig": "chr22_KI270733v1_random", "length": 179772}
- {"contig": "chr22_KI270734v1_random", "length": 165050}
- {"contig": "chr22_KI270735v1_random", "length": 42811}
- {"contig": "chr22_KI270736v1_random", "length": 181920}
- {"contig": "chr22_KI270737v1_random", "length": 103838}
- {"contig": "chr22_KI270738v1_random", "length": 99375}
- {"contig": "chr22_KI270739v1_random", "length": 73985}
- {"contig": "chrY_KI270740v1_random", "length": 37240}
- {"contig": "chrUn_KI270302v1", "length": 2274}
- {"contig": "chrUn_KI270304v1", "length": 2165}
- {"contig": "chrUn_KI270303v1", "length": 1942}
- {"contig": "chrUn_KI270305v1", "length": 1472}
- {"contig": "chrUn_KI270322v1", "length": 21476}
- {"contig": "chrUn_KI270320v1", "length": 4416}
- {"contig": "chrUn_KI270310v1", "length": 1201}
- {"contig": "chrUn_KI270316v1", "length": 1444}
- {"contig": "chrUn_KI270315v1", "length": 2276}
- {"contig": "chrUn_KI270312v1", "length": 998}
- {"contig": "chrUn_KI270311v1", "length": 12399}
- {"contig": "chrUn_KI270317v1", "length": 37690}
- {"contig": "chrUn_KI270412v1", "length": 1179}
- {"contig": "chrUn_KI270411v1", "length": 2646}
- {"contig": "chrUn_KI270414v1", "length": 2489}
- {"contig": "chrUn_KI270419v1", "length": 1029}
- {"contig": "chrUn_KI270418v1", "length": 2145}
- {"contig": "chrUn_KI270420v1", "length": 2321}
- {"contig": "chrUn_KI270424v1", "length": 2140}
- {"contig": "chrUn_KI270417v1", "length": 2043}
- {"contig": "chrUn_KI270422v1", "length": 1445}
- {"contig": "chrUn_KI270423v1", "length": 981}
- {"contig": "chrUn_KI270425v1", "length": 1884}
- {"contig": "chrUn_KI270429v1", "length": 1361}
- {"contig": "chrUn_KI270442v1", "length": 392061}
- {"contig": "chrUn_KI270466v1", "length": 1233}
- {"contig": "chrUn_KI270465v1", "length": 1774}
- {"contig": "chrUn_KI270467v1", "length": 3920}
- {"contig": "chrUn_KI270435v1", "length": 92983}
- {"contig": "chrUn_KI270438v1", "length": 112505}
- {"contig": "chrUn_KI270468v1", "length": 4055}
- {"contig": "chrUn_KI270510v1", "length": 2415}
- {"contig": "chrUn_KI270509v1", "length": 2318}
- {"contig": "chrUn_KI270518v1", "length": 2186}
- {"contig": "chrUn_KI270508v1", "length": 1951}
- {"contig": "chrUn_KI270516v1", "length": 1300}
- {"contig": "chrUn_KI270512v1", "length": 22689}
- {"contig": "chrUn_KI270519v1", "length": 138126}
- {"contig": "chrUn_KI270522v1", "length": 5674}
- {"contig": "chrUn_KI270511v1", "length": 8127}
- {"contig": "chrUn_KI270515v1", "length": 6361}
- {"contig": "chrUn_KI270507v1", "length": 5353}
- {"contig": "chrUn_KI270517v1", "length": 3253}
- {"contig": "chrUn_KI270529v1", "length": 1899}
- {"contig": "chrUn_KI270528v1", "length": 2983}
- {"contig": "chrUn_KI270530v1", "length": 2168}
- {"contig": "chrUn_KI270539v1", "length": 993}
- {"contig": "chrUn_KI270538v1", "length": 91309}
- {"contig": "chrUn_KI270544v1", "length": 1202}
- {"contig": "chrUn_KI270548v1", "length": 1599}
- {"contig": "chrUn_KI270583v1", "length": 1400}
- {"contig": "chrUn_KI270587v1", "length": 2969}
- {"contig": "chrUn_KI270580v1", "length": 1553}
- {"contig": "chrUn_KI270581v1", "length": 7046}
- {"contig": "chrUn_KI270579v1", "length": 31033}
- {"contig": "chrUn_KI270589v1", "length": 44474}
- {"contig": "chrUn_KI270590v1", "length": 4685}
- {"contig": "chrUn_KI270584v1", "length": 4513}
- {"contig": "chrUn_KI270582v1", "length": 6504}
- {"contig": "chrUn_KI270588v1", "length": 6158}
- {"contig": "chrUn_KI270593v1", "length": 3041}
- {"contig": "chrUn_KI270591v1", "length": 5796}
- {"contig": "chrUn_KI270330v1", "length": 1652}
- {"contig": "chrUn_KI270329v1", "length": 1040}
- {"contig": "chrUn_KI270334v1", "length": 1368}
- {"contig": "chrUn_KI270333v1", "length": 2699}
- {"contig": "chrUn_KI270335v1", "length": 1048}
- {"contig": "chrUn_KI270338v1", "length": 1428}
- {"contig": "chrUn_KI270340v1", "length": 1428}
- {"contig": "chrUn_KI270336v1", "length": 1026}
- {"contig": "chrUn_KI270337v1", "length": 1121}
- {"contig": "chrUn_KI270363v1", "length": 1803}
- {"contig": "chrUn_KI270364v1", "length": 2855}
- {"contig": "chrUn_KI270362v1", "length": 3530}
- {"contig": "chrUn_KI270366v1", "length": 8320}
- {"contig": "chrUn_KI270378v1", "length": 1048}
- {"contig": "chrUn_KI270379v1", "length": 1045}
- {"contig": "chrUn_KI270389v1", "length": 1298}
- {"contig": "chrUn_KI270390v1", "length": 2387}
- {"contig": "chrUn_KI270387v1", "length": 1537}
- {"contig": "chrUn_KI270395v1", "length": 1143}
- {"contig": "chrUn_KI270396v1", "length": 1880}
- {"contig": "chrUn_KI270388v1", "length": 1216}
- {"contig": "chrUn_KI270394v1", "length": 970}
- {"contig": "chrUn_KI270386v1", "length": 1788}
- {"contig": "chrUn_KI270391v1", "length": 1484}
- {"contig": "chrUn_KI270383v1", "length": 1750}
- {"contig": "chrUn_KI270393v1", "length": 1308}
- {"contig": "chrUn_KI270384v1", "length": 1658}
- {"contig": "chrUn_KI270392v1", "length": 971}
- {"contig": "chrUn_KI270381v1", "length": 1930}
- {"contig": "chrUn_KI270385v1", "length": 990}
- {"contig": "chrUn_KI270382v1", "length": 4215}
- {"contig": "chrUn_KI270376v1", "length": 1136}
- {"contig": "chrUn_KI270374v1", "length": 2656}
- {"contig": "chrUn_KI270372v1", "length": 1650}
- {"contig": "chrUn_KI270373v1", "length": 1451}
- {"contig": "chrUn_KI270375v1", "length": 2378}
- {"contig": "chrUn_KI270371v1", "length": 2805}
- {"contig": "chrUn_KI270448v1", "length": 7992}
- {"contig": "chrUn_KI270521v1", "length": 7642}
- {"contig": "chrUn_GL000195v1", "length": 182896}
- {"contig": "chrUn_GL000219v1", "length": 179198}
- {"contig": "chrUn_GL000220v1", "length": 161802}
- {"contig": "chrUn_GL000224v1", "length": 179693}
- {"contig": "chrUn_KI270741v1", "length": 157432}
- {"contig": "chrUn_GL000226v1", "length": 15008}
- {"contig": "chrUn_GL000213v1", "length": 164239}
- {"contig": "chrUn_KI270743v1", "length": 210658}
- {"contig": "chrUn_KI270744v1", "length": 168472}
- {"contig": "chrUn_KI270745v1", "length": 41891}
- {"contig": "chrUn_KI270746v1", "length": 66486}
- {"contig": "chrUn_KI270747v1", "length": 198735}
- {"contig": "chrUn_KI270748v1", "length": 93321}
- {"contig": "chrUn_KI270749v1", "length": 158759}
- {"contig": "chrUn_KI270750v1", "length": 148850}
- {"contig": "chrUn_KI270751v1", "length": 150742}
- {"contig": "chrUn_KI270752v1", "length": 27745}
- {"contig": "chrUn_KI270753v1", "length": 62944}
- {"contig": "chrUn_KI270754v1", "length": 40191}
- {"contig": "chrUn_KI270755v1", "length": 36723}
- {"contig": "chrUn_KI270756v1", "length": 79590}
- {"contig": "chrUn_KI270757v1", "length": 71251}
- {"contig": "chrUn_GL000214v1", "length": 137718}
- {"contig": "chrUn_KI270742v1", "length": 186739}
- {"contig": "chrUn_GL000216v2", "length": 176608}
- {"contig": "chrUn_GL000218v1", "length": 161147}
primary_calling_contigs:
# Contigs in the genome build that should be considered for variant calling
# Note that chrM is not included in this list because the mitochrondria
# should be analyzed separately.
- {"contig": chr1, "length": 248956422}
- {"contig": chr2, "length": 242193529}
- {"contig": chr3, "length": 198295559}
- {"contig": chr4, "length": 190214555}
- {"contig": chr5, "length": 181538259}
- {"contig": chr6, "length": 170805979}
- {"contig": chr7, "length": 159345973}
- {"contig": chr8, "length": 145138636}
- {"contig": chr9, "length": 138394717}
- {"contig": chr10, "length": 133797422}
- {"contig": chr11, "length": 135086622}
- {"contig": chr12, "length": 133275309}
- {"contig": chr13, "length": 114364328}
- {"contig": chr14, "length": 107043718}
- {"contig": chr15, "length": 101991189}
- {"contig": chr16, "length": 90338345}
- {"contig": chr17, "length": 83257441}
- {"contig": chr18, "length": 80373285}
- {"contig": chr19, "length": 58617616}
- {"contig": chr20, "length": 64444167}
- {"contig": chr21, "length": 46709983}
- {"contig": chr22, "length": 50818468}
- {"contig": chrX, "length": 156040895}
- {"contig": chrY, "length": 57227415}
calling_intervals:
# Calling contigs broken down into smaller batches of intervals. These intervals
# are taken from GATK Resource Bundle and describe regions that can be safely
# called independently for SNP/small indel genotyping.
# Removed the following interval batch as both of the intervals completely overlap with an interval in the ENCODE blacklist
# chr3:90568829-90722458
# chr3:90772459-91249905
- - {"contig": "chr1", "length": 197665, "start": 10001, "stop": 207666}
- {"contig": "chr1", "length": 40301, "start": 257667, "stop": 297968}
- {"contig": "chr1", "length": 188019, "start": 347969, "stop": 535988}
- {"contig": "chr1", "length": 2116792, "start": 585989, "stop": 2702781}
- {"contig": "chr1", "length": 10208093, "start": 2746291, "stop": 12954384}
- {"contig": "chr1", "length": 3794778, "start": 13004385, "stop": 16799163}
- {"contig": "chr1", "length": 12703069, "start": 16849164, "stop": 29552233}
- - {"contig": "chr1", "length": 92422623, "start": 29553836, "stop": 121976459}
- {"contig": "chr1", "length": 2951484, "start": 122026460, "stop": 124977944}
- {"contig": "chr1", "length": 151919, "start": 124978327, "stop": 125130246}
- {"contig": "chr1", "length": 39499, "start": 125131848, "stop": 125171347}
- {"contig": "chr1", "length": 11003, "start": 125173584, "stop": 125184587}
- - {"contig": "chr1", "length": 80374347, "start": 143184588, "stop": 223558935}
- {"contig": "chr1", "length": 4949428, "start": 223608936, "stop": 228558364}
- - {"contig": "chr1", "length": 20338057, "start": 228608365, "stop": 248946422}
- {"contig": "chr2", "length": 16135118, "start": 10001, "stop": 16145119}
- {"contig": "chr2", "length": 16721010, "start": 16146120, "stop": 32867130}
- {"contig": "chr2", "length": 47170, "start": 32868131, "stop": 32915301}
- - {"contig": "chr2", "length": 56413053, "start": 32917626, "stop": 89330679}
- {"contig": "chr2", "length": 155312, "start": 89530680, "stop": 89685992}
- {"contig": "chr2", "length": 648518, "start": 89753993, "stop": 90402511}
- {"contig": "chr2", "length": 735633, "start": 91402512, "stop": 92138145}
- {"contig": "chr2", "length": 1902411, "start": 92188146, "stop": 94090557}
- {"contig": "chr2", "length": 152457, "start": 94140558, "stop": 94293015}
- {"contig": "chr2", "length": 2943602, "start": 94496016, "stop": 97439618}
- - {"contig": "chr2", "length": 141414040, "start": 97489619, "stop": 238903659}
- - {"contig": "chr2", "length": 3279481, "start": 238904048, "stop": 242183529}
- - {"contig": "chr3", "length": 90555294, "start": 10001, "stop": 90565295}
- - {"contig": "chr3", "length": 1468, "start": 91256422, "stop": 91257890}
- {"contig": "chr3", "length": 5200, "start": 91260181, "stop": 91265381}
- {"contig": "chr3", "length": 5180, "start": 91276995, "stop": 91282175}
- {"contig": "chr3", "length": 2187625, "start": 91282735, "stop": 93470360}
- {"contig": "chr3", "length": 184773, "start": 93470801, "stop": 93655574}
- - {"contig": "chr3", "length": 104529984, "start": 93705575, "stop": 198235559}
- - {"contig": "chr4", "length": 1419357, "start": 10001, "stop": 1429358}
- {"contig": "chr4", "length": 1587, "start": 1434207, "stop": 1435794}
- {"contig": "chr4", "length": 7355924, "start": 1441553, "stop": 8797477}
- {"contig": "chr4", "length": 456438, "start": 8816478, "stop": 9272916}
- {"contig": "chr4", "length": 22496378, "start": 9322917, "stop": 31819295}
- {"contig": "chr4", "length": 1000446, "start": 31832570, "stop": 32833016}
- {"contig": "chr4", "length": 16497907, "start": 32839017, "stop": 49336924}
- {"contig": "chr4", "length": 171175, "start": 49486925, "stop": 49658100}
- {"contig": "chr4", "length": 2035850, "start": 49708101, "stop": 51743951}
- {"contig": "chr4", "length": 7084841, "start": 51793952, "stop": 58878793}
- - {"contig": "chr4", "length": 131201739, "start": 58921382, "stop": 190123121}
- - {"contig": "chr4", "length": 31433, "start": 190173122, "stop": 190204555}
- {"contig": "chr5", "length": 17520547, "start": 10001, "stop": 17530548}
- {"contig": "chr5", "length": 28855351, "start": 17580549, "stop": 46435900}
- {"contig": "chr5", "length": 583261, "start": 46485901, "stop": 47069162}
- {"contig": "chr5", "length": 6002, "start": 47073731, "stop": 47079733}
- {"contig": "chr5", "length": 218504, "start": 47082081, "stop": 47300585}
- {"contig": "chr5", "length": 2997, "start": 47306087, "stop": 47309084}
- {"contig": "chr5", "length": 1450, "start": 49591470, "stop": 49592920}
- {"contig": "chr5", "length": 3807, "start": 49599324, "stop": 49603131}
- {"contig": "chr5", "length": 2006, "start": 49609715, "stop": 49611721}
- {"contig": "chr5", "length": 6897, "start": 49612097, "stop": 49618994}
- {"contig": "chr5", "length": 6559, "start": 49621606, "stop": 49628165}
- {"contig": "chr5", "length": 3063, "start": 49630730, "stop": 49633793}
- {"contig": "chr5", "length": 8757, "start": 49641816, "stop": 49650573}
- {"contig": "chr5", "length": 5609, "start": 49656262, "stop": 49661871}
- {"contig": "chr5", "length": 393633, "start": 49666174, "stop": 50059807}
- - {"contig": "chr5", "length": 89342851, "start": 50109808, "stop": 139452659}
- - {"contig": "chr5", "length": 16306664, "start": 139453660, "stop": 155760324}
- {"contig": "chr5", "length": 25716934, "start": 155761325, "stop": 181478259}
- {"contig": "chr6", "length": 58393887, "start": 60001, "stop": 58453888}
- {"contig": "chr6", "length": 1276045, "start": 58553889, "stop": 59829934}
- - {"contig": "chr6", "length": 1127094, "start": 60229935, "stop": 61357029}
- {"contig": "chr6", "length": 7487, "start": 61363067, "stop": 61370554}
- {"contig": "chr6", "length": 33649417, "start": 61371373, "stop": 95020790}
- - {"contig": "chr6", "length": 72520602, "start": 95070791, "stop": 167591393}
- {"contig": "chr6", "length": 3104585, "start": 167641394, "stop": 170745979}
- {"contig": "chr7", "length": 227845, "start": 10001, "stop": 237846}
- - {"contig": "chr7", "length": 57879410, "start": 240243, "stop": 58119653}
- {"contig": "chr7", "length": 2658580, "start": 58169654, "stop": 60828234}
- {"contig": "chr7", "length": 449553, "start": 60878235, "stop": 61327788}
- {"contig": "chr7", "length": 150231, "start": 61377789, "stop": 61528020}
- {"contig": "chr7", "length": 386148, "start": 61578021, "stop": 61964169}
- {"contig": "chr7", "length": 9040, "start": 61967064, "stop": 61976104}
- {"contig": "chr7", "length": 430674, "start": 62026105, "stop": 62456779}
- - {"contig": "chr7", "length": 81144024, "start": 62506780, "stop": 143650804}
- {"contig": "chr7", "length": 15635168, "start": 143700805, "stop": 159335973}
- - {"contig": "chr8", "length": 7557126, "start": 60001, "stop": 7617127}
- {"contig": "chr8", "length": 4567217, "start": 7667128, "stop": 12234345}
- {"contig": "chr8", "length": 31699398, "start": 12284346, "stop": 43983744}
- {"contig": "chr8", "length": 1843520, "start": 44033745, "stop": 45877265}
- {"contig": "chr8", "length": 39736956, "start": 45927266, "stop": 85664222}
- - {"contig": "chr8", "length": 59364413, "start": 85714223, "stop": 145078636}
- {"contig": "chr9", "length": 41215985, "start": 10001, "stop": 41225986}
- {"contig": "chr9", "length": 8373, "start": 41229379, "stop": 41237752}
- - {"contig": "chr9", "length": 1983662, "start": 41238505, "stop": 43222167}
- {"contig": "chr9", "length": 27122, "start": 43236168, "stop": 43263290}
- {"contig": "chr9", "length": 7123, "start": 43263821, "stop": 43270944}
- {"contig": "chr9", "length": 1312, "start": 43274936, "stop": 43276248}
- {"contig": "chr9", "length": 4865, "start": 43276458, "stop": 43281323}
- {"contig": "chr9", "length": 49217, "start": 43282957, "stop": 43332174}
- {"contig": "chr9", "length": 37135, "start": 43333270, "stop": 43370405}
- {"contig": "chr9", "length": 6127, "start": 43371326, "stop": 43377453}
- {"contig": "chr9", "length": 2136278, "start": 43382280, "stop": 45518558}
- {"contig": "chr9", "length": 169873, "start": 60518559, "stop": 60688432}
- {"contig": "chr9", "length": 41088, "start": 60738433, "stop": 60779521}
- {"contig": "chr9", "length": 174365, "start": 60829522, "stop": 61003887}
- {"contig": "chr9", "length": 178078, "start": 61053888, "stop": 61231966}
- {"contig": "chr9", "length": 186841, "start": 61281967, "stop": 61468808}
- {"contig": "chr9", "length": 216559, "start": 61518809, "stop": 61735368}
- {"contig": "chr9", "length": 364369, "start": 61785369, "stop": 62149738}
- {"contig": "chr9", "length": 499093, "start": 62249739, "stop": 62748832}
- {"contig": "chr9", "length": 159538, "start": 62798833, "stop": 62958371}
- {"contig": "chr9", "length": 194490, "start": 63008372, "stop": 63202862}
- {"contig": "chr9", "length": 239401, "start": 63252863, "stop": 63492264}
- {"contig": "chr9", "length": 376182, "start": 63542265, "stop": 63918447}
- {"contig": "chr9", "length": 166565, "start": 63968448, "stop": 64135013}
- {"contig": "chr9", "length": 30148, "start": 64185014, "stop": 64215162}
- {"contig": "chr9", "length": 682961, "start": 64315163, "stop": 64998124}
- {"contig": "chr9", "length": 31957, "start": 65048125, "stop": 65080082}
- {"contig": "chr9", "length": 195040, "start": 65130083, "stop": 65325123}
- {"contig": "chr9", "length": 220067, "start": 65375124, "stop": 65595191}
- {"contig": "chr9", "length": 746195, "start": 65645192, "stop": 66391387}
- {"contig": "chr9", "length": 1329164, "start": 66591388, "stop": 67920552}
- {"contig": "chr9", "length": 65962539, "start": 68220553, "stop": 134183092}
- {"contig": "chr9", "length": 4149180, "start": 134185537, "stop": 138334717}
- - {"contig": "chr10", "length": 38519906, "start": 10001, "stop": 38529907}
- {"contig": "chr10", "length": 332697, "start": 38573339, "stop": 38906036}
- {"contig": "chr10", "length": 1857, "start": 38911581, "stop": 38913438}
- {"contig": "chr10", "length": 311648, "start": 38918270, "stop": 39229918}
- {"contig": "chr10", "length": 179655, "start": 39230137, "stop": 39409792}
- {"contig": "chr10", "length": 175049, "start": 39410238, "stop": 39585287}
- {"contig": "chr10", "length": 2577, "start": 39590436, "stop": 39593013}
- {"contig": "chr10", "length": 5263, "start": 39597436, "stop": 39602699}
- {"contig": "chr10", "length": 7099, "start": 39606090, "stop": 39613189}
- {"contig": "chr10", "length": 6734, "start": 39615619, "stop": 39622353}
- {"contig": "chr10", "length": 11407, "start": 39625275, "stop": 39636682}
- {"contig": "chr10", "length": 1906838, "start": 39686683, "stop": 41593521}
- {"contig": "chr10", "length": 222743, "start": 41693522, "stop": 41916265}
- {"contig": "chr10", "length": 5714102, "start": 42066266, "stop": 47780368}
- - {"contig": "chr10", "length": 76250831, "start": 47870369, "stop": 124121200}
- {"contig": "chr10", "length": 9568963, "start": 124121503, "stop": 133690466}
- {"contig": "chr10", "length": 46955, "start": 133740467, "stop": 133787422}
- - {"contig": "chr11", "length": 50761347, "start": 60001, "stop": 50821348}
- {"contig": "chr11", "length": 3346725, "start": 51078349, "stop": 54425074}
- {"contig": "chr11", "length": 16430621, "start": 54525075, "stop": 70955696}
- {"contig": "chr11", "length": 16922505, "start": 71055697, "stop": 87978202}
- - {"contig": "chr11", "length": 47073725, "start": 88002897, "stop": 135076622}
- {"contig": "chr12", "length": 7073649, "start": 10001, "stop": 7083650}
- {"contig": "chr12", "length": 27634756, "start": 7084651, "stop": 34719407}
- {"contig": "chr12", "length": 52881, "start": 34769408, "stop": 34822289}
- {"contig": "chr12", "length": 2356014, "start": 34829238, "stop": 37185252}
- {"contig": "chr12", "length": 5691, "start": 37235253, "stop": 37240944}
- {"contig": "chr12", "length": 9615, "start": 37245717, "stop": 37255332}
- {"contig": "chr12", "length": 122795, "start": 37257056, "stop": 37379851}
- - {"contig": "chr12", "length": 94842901, "start": 37380461, "stop": 132223362}
- {"contig": "chr12", "length": 1040946, "start": 132224363, "stop": 133265309}
- {"contig": "chr13", "length": 2051247, "start": 16000001, "stop": 18051248}
- {"contig": "chr13", "length": 186857, "start": 18171249, "stop": 18358106}
- - {"contig": "chr13", "length": 67794872, "start": 18408107, "stop": 86202979}
- {"contig": "chr13", "length": 25450875, "start": 86252980, "stop": 111703855}
- {"contig": "chr13", "length": 39585, "start": 111753856, "stop": 111793441}
- {"contig": "chr13", "length": 1829578, "start": 111843442, "stop": 113673020}
- {"contig": "chr13", "length": 631307, "start": 113723021, "stop": 114354328}
- {"contig": "chr14", "length": 31338, "start": 16022638, "stop": 16053976}
- {"contig": "chr14", "length": 7217, "start": 16054460, "stop": 16061677}
- {"contig": "chr14", "length": 24631, "start": 16061994, "stop": 16086625}
- {"contig": "chr14", "length": 15813, "start": 16089563, "stop": 16105376}
- {"contig": "chr14", "length": 17625, "start": 16113233, "stop": 16130858}
- {"contig": "chr14", "length": 7191, "start": 16133336, "stop": 16140527}
- {"contig": "chr14", "length": 4184, "start": 16400164, "stop": 16404348}
- {"contig": "chr14", "length": 489120, "start": 18223524, "stop": 18712644}
- {"contig": "chr14", "length": 649068, "start": 18862645, "stop": 19511713}
- - {"contig": "chr14", "length": 87272004, "start": 19611714, "stop": 106883718}
- {"contig": "chr15", "length": 2725253, "start": 17000001, "stop": 19725254}
- {"contig": "chr15", "length": 914049, "start": 19775255, "stop": 20689304}
- {"contig": "chr15", "length": 463743, "start": 20729747, "stop": 21193490}
- {"contig": "chr15", "length": 536411, "start": 21242091, "stop": 21778502}
- {"contig": "chr15", "length": 479739, "start": 21828503, "stop": 22308242}
- {"contig": "chr15", "length": 868631, "start": 22358243, "stop": 23226874}
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