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Test-drive the GATK tools and Best Practices pipelines on Terra
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Bug in GATK exome pipeline - VerifyBamID step
Hi, In the CheckContamination task of the gatk-workflows exome pipeline, there is a bug where VerifyBamID sometimes fails with the following error. Perhaps due to exome data inputs that are a bit smaller than what the Broad usually produces.
NOTICE - Process chr22:50683836-50683836...
NOTICE - Process chr22:50694325-50694325...
NOTICE - Process chr22:50745507-50745507...
NOTICE - Process chr22:50774185-50774185...
NOTICE - Number of marker in Reference Matrix:99976
NOTICE - Number of marker shared with input file:9565
NOTICE - Mean Depth:26.386618
NOTICE - SD Depth:43.449975
NOTICE - 9364 SNP markers remained after sanity check.
Insufficient Available markers, check input bam depth distribution in output pileup file after specifying --OutputPileup
2019/08/31 09:54:55 Starting delocalization.
2019/08/31 09:54:57 Delocalizing output /cromwell_root/UDP-1103.exome.preBqsr.selfSM -> gs://fc-secure-da2df7c1-77ef-4ed0-95ab-20cbed757a2a/95aed782-1446-4314-bb03-e9388219d197/ExomeGermlineSingleSample/b5e52cca-926e-44c1-8ddc-d55571b087ab/call-UnmappedBamToAlignedBam/UnmappedBamToAlignedBam/b6b3104e-8119-4636-8f04-7c601578ddf0/call-CheckContamination/UDP-1103.exome.preBqsr.selfSM
Required file output '/cromwell_root/UDP-1103.exome.preBqsr.selfSM' does not exist.