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Can I call SNPs from sex chromosomes and autosomes together in the same run?

Hi GATK authors,

My reference has autosomes, sex chromosomes, as well as mtDNAs. I'm not sure whether I could use UG or HC for SNP calling and genotyping together without additional settings and get the reasonable result?

Best,

Answers

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin

    Hi there,

    There is a brief discussion of how to deal with sex chromosomes in the Unified Genotyper Method documentation here:

    http://www.broadinstitute.org/gatk/guide/article?id=1237

    This should give you some pointers about how to deal with those chromosomes if you need to be able to call everything together (valid for both UG and HC). Or if you call X/Y and MT separately, you can tell the UnifiedGenotyper what ploidy to expect for those chromosomes. Note that the HC assumes ploidy=2 so if you want to run on Y alone, for example, it's better to use UG with ploidy=1 rather than HC.

  • skblazerskblazer Member

    Thanks for the information.

    "Our general approach to calling on X and Y is to treat them just as we do the autosomes and then applying a gender-aware tools to correct the genotypes afterwards."

    Does this mean if GATK could identify sex chromosomes from the autosome sequence set by itself and apply a gender-aware tool automatically independent of my settings? If this is true, how GATK did this? based on the estimated genotype likelihoods or just depends on the chromosome names? Only for chrX and chrY? If I worked on a non-human reference with other nomenclature if this still works?

    Best

    @Geraldine_VdAuwera said:
    Hi there,

    There is a brief discussion of how to deal with sex chromosomes in the Unified Genotyper Method documentation here:

    http://www.broadinstitute.org/gatk/guide/article?id=1237

    This should give you some pointers about how to deal with those chromosomes if you need to be able to call everything together (valid for both UG and HC). Or if you call X/Y and MT separately, you can tell the UnifiedGenotyper what ploidy to expect for those chromosomes. Note that the HC assumes ploidy=2 so if you want to run on Y alone, for example, it's better to use UG with ploidy=1 rather than HC.

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