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!

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.
We will be out of the office on October 14, 2019, due to the U.S. holiday. We will return to monitoring the forum on October 15.

StrandArtifect fields missed in normal sample in Mutect2 output

siriansirian USMember
edited June 2018 in Ask the GATK team

I used the latest version of Mutect2 to call somatic variants by comparing a tumor sample versus a normal sample. There is inconsistency of the fields between columns "FORMAT", "NORMAL" and "TUMOR". Taking one variant as an example:

1 3009350 . T TTG . . DP=59;ECNT=1;NLOD=2.46;N_ART_LOD=-9.935e-01;POP_AF=1.000e-05;RPA=26,27;RU=TG;STR;TLOD=10.24 GT:AD:AF:F1R2:F2R1:MBQ:MFRL:MMQ:MPOS:SA_MAP_AF:SA_POST_PROB 0/0:8,0:0.409:5,0:3,0:0:353,0:0:0 0/1:3,5:0.565:2,3:1,2:28:221,218:60:5:0.616,0.566,0.625:0.018,0.044,0.938

The last two fields "SA_MAP_AF" and "SA_POST_PROB" were calculated for only tumor sample (last column), but missed in normal sample (10th column), which resulted in discrepancy between FORMAT column and the normal sample column. Is it true that Mutect2 only reports them for tumor sample? If so, it'd be best to let Mutect2 print missing values (eg. a period) to fill the last two fields for normal sample.


  • SheilaSheila admin Broad InstituteMember, Broadie, Moderator admin


    I am pretty sure this is expected, but let me confirm with the team and get back to you.


  • SheilaSheila admin Broad InstituteMember, Broadie, Moderator admin

    Hi again,

    Do the dropped missing-value trailing fields cause a problem for downstream tools? Are these our tools?

    If you check the VCF spec, the trailing fields are allowed to be dropped.


Sign In or Register to comment.