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Mutect2 '-A StrandAlleleCountsBySample' option

jh2663jh2663 NYCMember
edited March 2016 in Ask the GATK team

I just noticed that Mutect2 doesn't include any strand allele counts info unlike HC when I add '-A StrandAlleleCountsBySample' option:

**AnnotationUtils - SAC annotation will not be calculated, must be called from HaplotypeCaller, not MuTect2 **

Then, how can I know strand bias information when using MuTect2? Or, doesn't MuTec2 have any internal filtering option based on strand bias yet?



  • SheilaSheila Broad InstituteMember, Broadie, Moderator admin


    You can use ALT_F1R2, ALT_F2R1, REF_F1R2, and REF_F2R1 as replacements for SAC.

    For a description of what those annotations are, have a look at the header. Also, this document should help with what the different orientations mean (under "Alignment Track").


    P.S. For a more in depth coverage, I hope this article will help as well.

  • jh2663jh2663 NYCMember
    edited March 2016

    Thank you for your answer. Here I attach an example showing something wrong in calculating ALT_F1R2 and ALT_F2R1 in MuTect2. The alignment in the locally re-assemblied BAM (by MuTect2) shows that all 12 reads are aligned one directional (reverse) but ALT_F1R2 and ALT_F2R1 counts in the vcf file are 9 and 3, respectively. This SNP is actually rejected by MuTect 1 due to 'strand_artifact' which looks right but passed in MuTect2. Is this a bug in the MuTect2?



  • SheilaSheila Broad InstituteMember, Broadie, Moderator admin


    I think Geraldine has responded here.


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