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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?
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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!