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If you happen to see a question you know the answer to, please do chime in and help your fellow community members. We encourage our fourm members to be more involved, jump in and help out your fellow researchers with their questions. GATK forum is a community forum and helping each other with using GATK tools and research is the cornerstone of our success as a genomics research community.We appreciate your help!
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HaplotypeCaller Missing variant with stand_call_conf 30
mehar
Member ✭✭
Dear GATK users,
I have a strange case to debug with HaplotypeCaller GATKv3.7 and -stand_call_conf 30 parameter. In essence, the below variant is found when -stand_call_conf 30 is not used and the variant is missing when -stand_call_conf 30 is used.
chr12 54677628 . G A 6505.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=-12.044;DP=486;ExcessHet=3.0103;FS=1.754;MLEAC=1;MLEAF=0.500;MQ=53.96;MQRankSum=-3.227;QD=13.41;ReadPosRankSum=0.672;SOR=0.835 GT:AD:DP:GQ:PL 0/1:261,224:485:99:6513,0,8151
Could someone explain how -stand_call_conf 30 is missing this variant despite of high depth and QUAL?
Tagged:
Answers
@mehar This does sound odd since the variant seems to have a pretty high QUAL score. Would you be able to post the entire command that you used so that we can help better trouble shoot?
@mehar
It looks like this may be a bug with GATK 3. Do you mind re-running with GATK 4.1 and reporting back if you are still seeing the same error? Thank you!