| Tool | Version | Task | Version |
|---|---|---|---|
| Utilities | NA | findFiles | 0.0.2 |
| convertBedToIntervals | 0.0.1 | ||
| makeLink | 0.0.1 | ||
| concatenateFiles | 0.0.2 | ||
| wget | 0.0.1 | ||
| gzip | 0.0.1 | ||
| sortgtf | 0.0.1 | ||
| fai2bed | 0.0.1 | ||
| nanoVar2Bed | 0.0.4 | ||
| bed2Array | 0.0.1 | ||
| bedPrimer2woutPrimer | 0.0.1 | ||
| getColumn | 0.0.2 | ||
| filterBEDOnName | 0.0.2 | ||
| Anacore Utils | 3.3.0 | nonOverlappingDesign | 0.0.1 |
| addAmpliRG | 0.0.1 | ||
| areaCoverage | 0.0.1 | ||
| splitBAMByRG | 0.0.3 | ||
| filterVCFPrimers | 0.0.2 | ||
| addRGOnBAM | 0.0.2 | ||
| mergeVCFAmpli | 0.0.1 | ||
| meltVCFSamples | 0.0.1 | ||
| fixVCallerVCF | 0.0.1 | ||
| filterVCFOnCount | 0.0.1 | ||
| sortVCF | 0.0.1 | ||
| bedtools | v2.29.2 | intersect | 0.0.1 |
| sort | 0.0.1 | ||
| coverage | 0.0.2 | ||
| bgzip | 1.10.2 | compress | 0.0.2 |
| decompress | 0.0.2 | ||
| bcftools | 1.10.2 | index | 0.0.1 |
| merge | 0.0.1 | ||
| norm | 0.0.1 | ||
| stats | 0.0.1 | ||
| view | 0.0.1 | ||
| BWA | 0.7.17-r1188 | mem | 0.0.2 |
| index | 0.0.1 | ||
| Crumble | 0.8.3 | crumble | 0.0.1 |
| CLAIR | 2.1.1 | callVarBam | 0.0.7 |
| Cutadapt | 2.10 | adaptersTrimming | 0.0.2 |
| qualityTrimming | 0.0.2 | ||
| hardTrimming | 0.0.3 | ||
| DWGSim | 0.1.11 | simulateReadsIllumina | 0.0.1 |
| Fastp | v0.20.1 | fastp_pe | 0.0.1 |
| FastQC | v0.11.9 | fastqc | 0.0.1 |
| fastqcNano | 0.0.1 | ||
| fastqcCasava | 0.0.1 | ||
| GATK4 | v4.1.8.1 | ApplyBQSR | 0.0.2 |
| BaseRecalibrator | 0.0.2 | ||
| BedToIntervalList | 0.0.1 | ||
| IntervalListToBed | 0.0.1 | ||
| HaplotypeCaller | 0.0.7 | ||
| CollectMultipleMetrics | 0.0.1 | ||
| GatherBamFiles | 0.0.3 | ||
| GatherBQSRReports | 0.0.2 | ||
| GatherVcfFiles | 0.0.3 | ||
| LeftAlignIndels | 0.0.1 | ||
| ReorderSam | 0.0.1 | ||
| DepthOfCoverage (BETA) | 0.0.1 | ||
| SplitIntervals | 0.0.1 | ||
| SplitVcfs | 0.0.2 | ||
| VariantFiltration | 0.0.6 | ||
| MergeVcfs | 0.0.1 | ||
| SortVcf | 0.0.1 | ||
| SplitNCigarReads | 0.0.2 | ||
| RevertSam | 0.0.1 | ||
| SamToFastq | 0.0.1 | ||
| MarkDuplicates | 0.0.1 | ||
| Longshot | 0.4.1 | longshot | 0.0.3 |
| MiniMap2 | 1.1.2 | mapOnt | 0.0.1 |
| MPA | 1.1.2 | mpa | 0.0.1 |
| NanoPlot | 1.36.2 | nanoplot_summary | 0.0.1 |
| nanoplot_fastq | 0.0.1 | ||
| Qualimap | v.2.2.2-dev | bamqc | 0.0.1 |
| Regtools | 0.5.2 | junctionsExtract | 0.0.1 |
| junctionsAnnotate | 0.0.1 | ||
| Rsync | 3.1.3 | rsync | 0.0.1 |
| RTG tools | 3.12 | fasta2sdf | 0.0.1 |
| vcfeval | 0.0.1 | ||
| Sambamba | 0.7.1 | index | 0.0.2 |
| flagstat | 0.0.1 | ||
| markdup | 0.0.1 | ||
| sort | 0.0.2 | ||
| view | 0.0.2 | ||
| Samtools | 1.10 | bedcov | 0.0.1 |
| index | 0.0.1 | ||
| flagstat | 0.0.1 | ||
| sort | 0.0.1 | ||
| dict | 0.0.1 | ||
| view | 0.0.1 | ||
| faidx | 0.0.1 | ||
| fqidx | 0.0.1 | ||
| markdup | 0.0.1 | ||
| fixmate | 0.0.1 | ||
| merge | 0.0.1 | ||
| depth | 0.0.4 | ||
| Sed | 4.8 | sedReplace | 0.0.1 |
| getExpressionFromString | 0.0.2 | ||
| SeqKit | 0.16.0 | seq_filter | 0.0.1 |
| snpEff | 5.0 | install | 0.0.1 |
| Star | 2.7.5c | genomeGenerate | 0.0.1 |
| alignReads | 0.0.5 | ||
| Tabix | 1.10.2 | index | 0.0.1 |
| Vardict-java | 1.8.2 | vardictSoloAmplicons | 0.0.4 |
| teststrandbias | 0.0.2 | ||
| var2vcf_valid | 0.0.2 | ||
| VEP | 101.0 | vep_cache | 0.0.2 |
| install | 0.0.1 |