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crosscheckFingerprints

Checks if all the genetic data within a set of files appear to come from the same individual by using Picard CrosscheckFingerprints

Overview

Dependencies

Usage

Cromwell

java -jar cromwell.jar run crosscheckFingerprints.wdl --inputs inputs.json

Inputs

Required workflow parameters:

Parameter Value Description
inputs Array[File] A list of SAM/BAM/VCF files to fingerprint.
haplotypeMapFileName String The file name that lists a set of SNPs, optionally arranged in high-LD blocks, to be used for fingerprinting.

Optional workflow parameters:

Parameter Value Default Description
haplotypeMapDir String "$CROSSCHECKFINGERPRINTS_HAPLOTYPE_MAP_ROOT" The directory that contains haplotype map files. By default the modulator data directory.
outputPrefix String "output" Text to prepend to all output.

Optional task parameters:

Parameter Value Default Description
runCrosscheckFingerprints.crosscheckBy String "READGROUP" Specificies which data-type should be used as the basic comparison unit. Fingerprints from readgroups can be 'rolled-up' to the LIBRARY, SAMPLE, or FILE level before being compared. Fingerprints from VCF can be be compared by SAMPLE or FILE.
runCrosscheckFingerprints.picardMaxMemMb Int 3000 Passed to Java -Xmx (in Mb).
runCrosscheckFingerprints.exitCodeWhenMismatch Int 0 When one or more mismatches between groups is detected, exit with this value instead of 0.
runCrosscheckFingerprints.exitCodeWhenNoValidChecks Int 0 When all LOD score are zero, exit with this value.
runCrosscheckFingerprints.lodThreshold Float 0.0 If any two groups (with the same sample name) match with a LOD score lower than the threshold the tool will exit with a non-zero code to indicate error. Program will also exit with an error if it finds two groups with different sample name that match with a LOD score greater than -LOD_THRESHOLD. LOD score 0 means equal likelihood that the groups match vs. come from different individuals, negative LOD score -N, mean 10^N time more likely that the groups are from different individuals, and +N means 10^N times more likely that the groups are from the same individual.
runCrosscheckFingerprints.validationStringency String "SILENT" Validation stringency for all SAM files read by this program. Setting stringency to SILENT can improve performance when processing a BAM file in which variable-length data (read, qualities, tags) do not otherwise need to be decoded. See https://jira.oicr.on.ca/browse/GC-8372 for why this is set to SILENT for OICR purposes.
runCrosscheckFingerprints.modules String "gatk/4.2.0.0 crosscheckfingerprints-haplotype-map/20230324" Modules to load for this workflow.
runCrosscheckFingerprints.threads Int 4 Requested CPU threads.
runCrosscheckFingerprints.jobMemory Int 6 Memory (GB) allocated for this job.
runCrosscheckFingerprints.timeout Int 6 Number of hours before task timeout.

Outputs

Output Type Description Labels
crosscheckMetrics File The crosschecksMetrics file produced by Picard CrosscheckFingerprints vidarr_label: crosscheckMetrics
crosscheckMetricsMatrix File Matrix of LOD scores. This is less informative than the metrics output and only contains Normal-Normal LOD score (i.e. doesn't account for Loss of Heterozygosity. vidarr_label: crosscheckMetricsMatrix

Support

For support, please file an issue on the Github project or send an email to [email protected] .

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