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Should I use GATK haplotype caller/unified genotyper for finding SNPs in 2 whole genome bacterias?

NandaNanda CanadaMember

I have two whole genome sequenced bacterial samples. I have their contigs file with me. I would like to pairwise comparison between isolate1 and isolate2 to identify SNPs between them. Should I use GATK haplotype caller/unified genotyper for finding SNPs?


  • bhanuGandhambhanuGandham Cambridge MAMember, Administrator, Broadie, Moderator admin

    HI @Nanda

    I would recommend using Mutect2. Unified genotyper is a deprecated tool and is not supported by us anymore. Also we are in the process of creating a variant calling pipeline for bacterial isolates. If you are willing to share how Mutect2 works on your data i.e. what varianst it is calling and which ones it isn't, it might help us in our efforts.

  • NandaNanda CanadaMember

    Thanks, bhanu for getting back to me on my query. But Mutect2 is developed for tumor and non-tumor kind samples, Am I correct? Does Mutect2 provide the option of selecting the ploidy as 1 for bacteria.

    In my case, I am planning to compare bacterial isolateA and bacterial isolateB and then find SNPs between isolateA and isolateB.

  • bhanuGandhambhanuGandham Cambridge MAMember, Administrator, Broadie, Moderator admin
    edited August 26


    While HaplotypeCaller relies on a fixed ploidy assumption to calculate the genotype likelihoods that are the basis for genotype probabilities (PL), Mutect2 allows for varying ploidy in the form of allele fractions for each variant. Varying allele fractions are often seen within a tumor sample due to fractional purity, multiple subclones and copy number variation.

    For a single bacterial species HaplotypeCaller is correct for most purposes. If you are specifically interested in diversity (either a metagenome or just variation within a sample of cells from a single species) Mutect2 may be appropriate. I must admit that we have never tried Mutect2 on bacteria, but we would be interested in supporting any users who want to try! You could try running Mutect2 in tumor only mode for both isolates and compare the SNPs.

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