Test-drive the GATK tools and Best Practices pipelines on Terra
Check out this blog post to learn how you can get started with GATK and try out the pipelines in preconfigured workspaces (with a user-friendly interface!) without having to install anything.
HaplotypeCaller Missing variant with stand_call_conf 30
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?