Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

hiConfDeNovo \ loConfDeNovo bug #308

Open
gordonmi opened this issue Feb 10, 2019 · 0 comments
Open

hiConfDeNovo \ loConfDeNovo bug #308

gordonmi opened this issue Feb 10, 2019 · 0 comments

Comments

@gordonmi
Copy link

bug with loConfDeNovo/hiConfDeNovo field
In case of more than one sample with de novo mutation (sep by ","), report only the first one. The fields loConfDeNovo/hiConfDeNovo generated by GATK Genotype Refinement workflow (PossibleDeNovo)

e.g.
2 203417403 . A T 201.07 PASS AC=2;AF=5.291e-03;AN=378;BaseQRankSum=0.260;DP=8232;FS=0.000;InbreedingCoeff=-0.0178;MLEAC=3;MLEAF=7.937e-03;MQ=59.22;MQRankSum=0.154;PG=0,18,41;QD=0.97;ReadPosRankSum=0.543;SOR=0.607;VQSLOD=3.67;culprit=QD;hiConfDeNovo=SAMPLE-1,SAMPLE-2 GT:AD:DP:FT:GQ:JL:JP:PGT:PID:PL:PP 0/0:29,0:29:PASS:99:4:4:.:.:0,84,995:0,103,1045 0/0:35,3:38:PASS:25:4:4:1|0:203417391_AT_A:0,7,1149:0,25,1250 0/0:53,5:58:lowGQ:13:4:4:.:.:5,0,1737:0,13,1833

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
None yet
Projects
None yet
Development

No branches or pull requests

1 participant