Registry.hub.docker.com/pfda2dockstore/gatk-hs37d5decoy-hardfilter/gatk-hs37d5decoy-hardfilter

Automatic Tools and Workflows
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This app was exported from precisionFDA (https://precision.fda.gov).
It was created by Justin Zook, NIST.

HaplotypeCaller

Call germline SNPs and indels via local re-assembly of haplotypes.

Offical documentation: https://software.broadinstitute.org/gatk/gatkdocs/org_broadinstitute_gatk_tools_walkers_haplotypecaller_HaplotypeCaller.php

Modified to use GRCh37 with hs37d5 reference

Filter using default hard filters recommended by GATK best practices:

SNPS: --filterExpression "QD < 2.0 ||

This is a companion discussion topic for the original entry at registry.hub.docker.com/pfda2dockstore/gatk-hs37d5decoy-hardfilter/gatk-hs37d5decoy-hardfilter