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.
StrandArtifect fields missed in normal sample in Mutect2 output
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.