Default Mutect2 INFO field discrepancies between version 4.1.5.0 and 4.1.8.0

[slw287r]

Bug Report

Affected tool(s) or class(es)

Mutect2

Affected version(s)

• [ ] 4.1.5.0
• [x] 4.1.8.0

Description

INFO	4.1.5	4.1.8
AS_SB_TABLE	❌	✅
CONTQ	✅	❌
ClippingRankSum	✅	❌
DP	✅	✅
ECNT	✅	✅
GERMQ	✅	❌
MBQ	✅	✅
MFRL	✅	✅
MMQ	✅	✅
MPOS	✅	✅
PON	✅	✅
POPAF	✅	✅
ROQ	✅	❌
SEQQ	✅	❌
STRANDQ	✅	❌
TLOD	✅	✅

• 4.1.5.0

--annotation,-A:String        One or more specific annotations to add to variant calls  This argument may be specified 0
                              or more times. Default value: null. Possible Values: {AlleleFraction,
                              AS_BaseQualityRankSumTest, AS_FisherStrand, AS_InbreedingCoeff,
                              AS_MappingQualityRankSumTest, AS_QualByDepth, AS_ReadPosRankSumTest, AS_RMSMappingQuality,
                              AS_StrandOddsRatio, BaseQuality, BaseQualityHistogram, BaseQualityRankSumTest,
                              ChromosomeCounts, ClippingRankSumTest, CountNs, Coverage, DepthPerAlleleBySample,
                              DepthPerSampleHC, ExcessHet, FisherStrand, FragmentLength, GenotypeSummaries,
                              InbreedingCoeff, LikelihoodRankSumTest, MappingQuality, MappingQualityRankSumTest,
                              MappingQualityZero, OrientationBiasReadCounts, OriginalAlignment, PossibleDeNovo,
                              QualByDepth, ReadPosition, ReadPosRankSumTest, ReferenceBases, RMSMappingQuality,
                              SampleList, StrandBiasBySample, StrandOddsRatio, TandemRepeat, UniqueAltReadCount}

• 4.1.8.0

--annotation,-A:String        One or more specific annotations to add to variant calls  This argument may be specified 0
                              or more times. Default value: null. Possible values: {AlleleFraction,
                              AS_BaseQualityRankSumTest, AS_FisherStrand, AS_InbreedingCoeff,
                              AS_MappingQualityRankSumTest, AS_QualByDepth, AS_ReadPosRankSumTest, AS_RMSMappingQuality,
                              AS_StrandBiasMutectAnnotation, AS_StrandOddsRatio, BaseQuality, BaseQualityHistogram,
                              BaseQualityRankSumTest, ChromosomeCounts, ClippingRankSumTest, CountNs, Coverage,
                              DepthPerAlleleBySample, DepthPerSampleHC, ExcessHet, FisherStrand, FragmentLength,
                              GenotypeSummaries, InbreedingCoeff, LikelihoodRankSumTest, MappingQuality,
                              MappingQualityRankSumTest, MappingQualityZero, OrientationBiasReadCounts,
                              OriginalAlignment, PossibleDeNovo, QualByDepth, ReadPosition, ReadPosRankSumTest,
                              ReferenceBases, RMSMappingQuality, SampleList, StrandBiasBySample, StrandOddsRatio,
                              TandemRepeat, UniqueAltReadCountPossible values: {

We'd like to get back the missing ones in 4.1.8.0. Are they still being supported or how to achieve that?

Thanks, Richard

[droazen]

@fleharty Care to comment on this one?

[fleharty]

looking into this

[yl-h]

I would also like to have the missing annotations (they are only in the header in 4.1.8.0 VCF outputs).

The problem seems to be related to the changes in commit 3021e69 (mitochondrial pipeline, #6399) as running FilterMutectCalls on the previous commit c918f85 emits the annotations CONTQ, GEMRQ, etc.

[droazen]

@ahaessly Can you comment on whether your changes in https://github.com/broadinstitute/gatk/pull/6399 had the side effect of changing the default Mutect2 annotations?

[biounix]

Any update on that? The issue still persists in 4.2.6.1 two years later.

Thanks.