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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

Answers

  • 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;

    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 )

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