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.

filtering based on AD

BogdanBogdan Palo Alto, CAMember ✭✭

Dear Sheila, and Geraldine,

a piece of advice please : considering a following somatic mutation predicted by MUTECT2, what is the appropriate way to filter based on AD (allelic depth) :

**chr21 46689620 . G A . PASS BaseCounts=7,0,27,0;ECNT=1;FS=0.000;HCNT=1;HRun=4;MAX_ED=.;MIN_ED=.;MQ=33.87;NLOD=6.16;SOR=2.636;TLOD=10.90;VariantType=SNP GT:AD:AF:ALT_F1R2:ALT_F2R1:FOXOG:QSS:REF_F1R2:REF_F2R1 0/1:20,6:0.240:5:1:0.833:408,145:8:12 0/0:21,0:0.00:0:0:.:435,0:11:10
i.e. in the TUMOR, the AD is 20,6
in the NORMAL, AD is 21,1.

I would like the filter based on AD of "21,0" (instead of "21,1") i.e. to have 0 bases of the alternate allele in the NORMAL sample.
How could I do that ? Many thanks,

-- bogdan

Best Answer


  • BogdanBogdan Palo Alto, CAMember ✭✭

    Ahaaa ! 've just realized now that I could use the fields : ALT_F1R2:ALT_F2R and REF_F1R2:REF_F2R1 for doing the filtering I have intended to.

  • BogdanBogdan Palo Alto, CAMember ✭✭

    and then the question becomes -- are these fields ALT_F1R2:ALT_F2R and REF_F1R2:REF_F2R1 used to compute the SOR :

    if SOR=(REF_+strand * ALT_-strand) / ( REF_-strand * ALT_+strand)

    then SOR=(81 / (512) =0.13. Although in the VCF field, the SOR=2.63 ?

    ( chr21 46689620 . G A . PASS

    BaseCounts=7,0,27,0; ECNT=1;FS=0.000;




    0/0:21,0:0.00:0:0:.:435,0:11:10 )

Sign In or Register to comment.