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can mutect2 or haplotcaller call some specified sites list

hi, sometimes we are interested in some important gene sites, which maybe not PASS in mutect2 or haplotcaller, so is there a argument to add this site list, not all sites, but just these sites

thanks a lot

Best Answer


  • bklein345bklein345 Member

    check out the arguments --genotyping_mode GENOTYPE_GIVEN_ALLELES and --alleles your_alleles.vcf

  • 29043594952904359495 Member
    edited April 10

    @bklein345 Thanks for your attention.
    I ever searched some answers

    but I see 4.11.0 and, there is obvious different description here, and both version can not find --genotyping_mode is GENOTYPE_GIVEN_ALLELES, where is the argument of genotyping_mode, does it still exist in

    what is more, no matter in which version of haplotcaller, the description is "The set of alleles at which to genotype when --genotyping_mode is GENOTYPE_GIVEN_ALLELES"

    another important things is ""

    another important things is that it is the first time that mutect2 separately describe force mode,
    have you ever tried this, because it needs a vcf file, force-call-alleles.vcf, so do you know the format of that, usually we have a bed file of the hotsites that we want to call.

    the most important thing is that davidben seems to not support this --alleles , I do not know whether --alleles can be really used in both mutect2 andd haplttypecaller

    thanks a lot

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