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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.

Answers

  • SheilaSheila admin Broad InstituteMember, Broadie, Moderator admin

    @sirian
    Hi,

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

    -Sheila

  • SheilaSheila admin Broad InstituteMember, Broadie, Moderator admin

    @sirian
    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.

    Thanks,
    Sheila

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