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Can mutect2 be used for sequence data from pooled-Seq?

Hi, I am using Haplotype caller to call variants from WGS samples on pooled individuals. I wonder if there is a benefit to using Mutect2 in this case? Is it better controlling for ploidy effects somehow given that it can be used for cancer genomes?


  • shleeshlee CambridgeMember, Broadie, Moderator

    Hi @arunkuma,

    The HaplotypeCaller doc says:

    This tool is able to handle almost any ploidy (except very high ploidies in large pooled experiments); the ploidy can be specified using the -ploidy argument for non-diploid organisms.

    So if you have a rather large pooled experiment, MuTect2 may be preferable as it is highly sensitive and can call low allele fraction variants.

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