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about Variant Annotator and MUTATIONS (SNV/INDELS)

BogdanBogdan Palo Alto, CAMember ✭✭

Dear Sheila, and Geraldine,

would appreciate please a piece of advice : what tool could I use to COUNT the number of READS on FORWARD and REVERSE strand, for REFERENCE or ALTERNATE alleles, for a specific SNV or INDEL ? thank you,

bogdan

Comments

  • SheilaSheila Broad InstituteMember, Broadie ✭✭✭✭✭

    @Bogdan
    Hi Bogdan,

    There is no tool specifically to do that, but you can use the StrandAlleleCountsBySample annotation.

    -Sheila

  • BogdanBogdan Palo Alto, CAMember ✭✭

    Sheila, thanks ! I was hoping to be able to use StrandAlleleCountsBySample on VCF files that are produced by Mutect2;
    on the page that you had cited, it says "This annotation can only be generated by HaplotypeCaller (it will not work when called from VariantAnnotator)."

  • SheilaSheila Broad InstituteMember, Broadie ✭✭✭✭✭

    @Bogdan
    Hi Bogdan,

    Ah yes, the annotation documentation was written before Mutect2 was part of GATK. We will try to document the MuTect2 annotations soon. In the meantime, you can try the HaplotypeCaller annotations and let us know if you need one that is not working.

    -Sheila

  • BogdanBogdan Palo Alto, CAMember ✭✭

    great, thanks !

  • BogdanBogdan Palo Alto, CAMember ✭✭

    Hi Sheila,

    thanks, yes, I am able to get in the final MUTECT2 output the following fields : FS, MQRankSum, ReadPosRankSum , SOR.

    chr21 46689620 . G A . PASS ECNT=1;FS=2.433;HCNT=1;MAX_ED=.;MIN_ED=.;MQ=45.70;MQRankSum=-3.331;NLOD=6.16;ReadPosRankSum=-0.654;SOR=1.489;TLOD=10.90 GT:AD:AF:BCS 0/1:.:0.24
    0:857,246,552,543 0/0:21,0:0.00:690,201,450,431

    still have some question, although will open a new track ;)

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