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[kibanez]

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Bug Report

Affected tool(s)

picard-tools LiftoverVcf

Affected version(s)

• Latest v3.0.0 version
• v2.27.4

Unffected version

• v2.18.25

Description

_This issue is an edge case, but it happens with latest Picard-tools releases. With the release we started using picard-tools LiftoverVcf (v2.18.25) does not happen, but it does with >=v2.27.4. Affected VCF files are those processed by GATK with an Indel shown with *

Example:
chr21 10569528 . AG * 221.62 ExcessHet AC=1;AF=0.5;AN=2;BaseQRankSum=2.45;DP=89;ExcessHet=62.0242;FS=1.366;InbreedingCoeff=-0.5844;MQ=59.68;MQRankSum=0.757;QD=0.03;ReadPosRankSum=-0.662;SOR=0.795 GT:AD:DP:GQ:PL 0/1:73,16:89:99:441,0,2975
chr21 10569528 . AG A 221.62 ExcessHet AC=0;AF=0;AN=2;BaseQRankSum=2.45;DP=89;ExcessHet=62.0242;FS=1.366;InbreedingCoeff=-0.5844;MQ=59.68;MQRankSum=0.757;QD=0.03;ReadPosRankSum=-0.662;SOR=0.795 GT:AD:DP:GQ:PL 0/0:73,0:89:99:441,660,3683

with (unaffected) v2.18.25 we get

chr21 10942927 . TC T 221.62 ExcessHet AC=1;AF=0.5;AN=2;BaseQRankSum=2.45;DP=89;ExcessHet=62.0242;FS=1.366;InbreedingCoeff=-0.5844;MQ=59.68;MQRankSum=0.757;OriginalContig=chr21;OriginalStart=10569528;QD=0.03;ReadPosRankSum=-0.662;ReverseComplementedAlleles;SOR=0.795 GT:AD:DP:GQ:P0/1:73,16:89:99:441,0,2975

chr21 10942927 . TC T 221.62 ExcessHet AC=0;AF=0;AN=2;BaseQRankSum=2.45;DP=89;ExcessHet=62.0242;FS=1.366;InbreedingCoeff=-0.5844;MQ=59.68;MQRankSum=0.757;OriginalContig=chr21;OriginalStart=10569528;QD=0.03;ReadPosRankSum=-0.662;ReverseComplementedAlleles;SOR=0.795 GT:AD:DP:GQ:P0/0:73,0:89:99:441,660,3683

but with (affected) latest (v3.3.0) and v2.27.4 releases we get:

proband_b37_picard_2.27.vcf:chr21 1 . N * 221.62 ExcessHet AC=1;AF=0.5;AN=2;BaseQRankSum=2.45;DP=89;ExcessHet=62.0242;FS=1.366;InbreedingCoeff=-0.5844;MQ=59.68;MQRankSum=0.757;OriginalContig=chr21;OriginalStart=10569528;QD=0.03;ReadPosRankSum=-0.662;ReverseComplementedAlleles;SOR=0.795 GT:AD:DP:GQ:PL 0/1:73,16:89:99:441,0,2975
chr21 10942927 . TC T 221.62 ExcessHet AC=0;AF=0;AN=2;BaseQRankSum=2.45;DP=89;ExcessHet=62.0242;FS=1.366;InbreedingCoeff=-0.5844;MQ=59.68;MQRankSum=0.757;OriginalContig=chr21;OriginalStart=10569528;QD=0.03;ReadPosRankSum=-0.662;ReverseComplementedAlleles;SOR=0.795 GT:AD:DP:GQ:PL 0/0:73,0:89:99:441,660,3683

proband_b37_picard_2.27.vcf:

proband_b37_picard_2.27.vcf:chr21 1 . N * 221.62 ExcessHet AC=1;AF=0.5;AN=2;BaseQRankSum=2.45;DP=89;ExcessHet=62.0242;FS=1.366;InbreedingCoeff=-0.5844;MQ=59.68;MQRankSum=0.757;OriginalContig=chr21;OriginalStart=10569528;QD=0.03;ReadPosRankSum=-0.662;ReverseComplementedAlleles;SOR=0.795 GT:AD:DP:GQ:PL 0/1:73,16:89:99:441,0,2975
proband_b37_picard_2.27.vcf:chr21 10942927 . TC T 221.62 ExcessHet AC=0;AF=0;AN=2;BaseQRankSum=2.45;DP=89;ExcessHet=62.0242;FS=1.366;InbreedingCoeff=-0.5844;MQ=59.68;MQRankSum=0.757;OriginalContig=chr21;OriginalStart=10569528;QD=0.03;ReadPosRankSum=-0.662;ReverseComplementedAlleles;SOR=0.795 GT:AD:DP:GQ:PL 0/0:73,0:89:99:441,660,3683

Please, note that the original chr21:10569528:AG>* may cause picard-tools LiftoverVcf creating chr21:1:N>* ??
_

Steps to reproduce

_picard-tools LiftoverVcf
I=proband.vcf
O=proband_b37.vcf
CHAIN=/home/data/template/chain/hg38ToHg19.over.chain.gz
REJECT=proband_rejected.vcf
R=/home/data/fasta/hg19/hg19.fa
WRITE_ORIGINAL_POSITION=true

with any version >= v2.27.4
_

Expected behavior

Expected output should be similar to what v2.18.25 generates

Actual behavior

The new output creates (we think this is an edge case) POS == 1 in that chromosome. Only seen in one INDEL so far

[kachulis]

@kibanez thanks for the heads up about this! This should be fixed now if you want to build from source. Or the fix should be available in the next release.