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StrandArtifect fields missed in normal sample in Mutect2 output
sirian
USMember ✭
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
@sirian
Hi,
I am pretty sure this is expected, but let me confirm with the team and get back to you.
-Sheila
@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