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gatk-workflows / five-dollar-genome-analysis-pipeline

Workflows used for WGS data processing -- replaced by https://github.com/gatk-workflows/gatk4-genome-processing-pipeline
https://gatk.broadinstitute.org/hc/en-us
BSD 3-Clause "New" or "Revised" License
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What is "fingerprint_genotypes_file" #20

Closed JavisPeng closed 5 years ago

JavisPeng commented 5 years ago

I'm curious what's fingerprint_genotypes_file, which wdl file it appears in ?

"WholeGenomeGermlineSingleSample.references": {
    "fingerprint_genotypes_file": "gs://dsde-data-na12878-public/NA12878.hg38.reference.fingerprint.vcf",
    "fingerprint_genotypes_index": "gs://dsde-data-na12878-public/NA12878.hg38.reference.fingerprint.vcf.idx",
bshifaw commented 5 years ago

The following material is provided by the GATK Team. Please post any questions or concerns to one of our forum sites : GATK , FireCloud or Terra , WDL/Cromwell.

Fingerprint genotype file is "essentially, genotype information from different parts of the genome", The file your passing to the workflow here is the fingerprint you want to compare your sample VCF to. The file is used in the Qc.wdl subworkflow by the following tools: CheckFingerprint and CrosscheckFingerprints. The workflow that calls the tasks in the qc.wdl is the AggregatedBamQC.wdl wdl.

Please direct questions to