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GATK UGT -heterozygosity / -hets

kumar35885kumar35885 Member
edited October 2012 in Ask the GATK team

I have an inbred mouse strain that I am sequencing and there should be little to NO heterozygosity. Yet with the default settings of UGT -heterozygosity (which is 0.001) many homs are being called as hets. When 230/250 reads are alternate and 20/250 are reference, it calls a het, even though it should be homozygous alternate.

What do you recommendations for this setting for inbred animals?

thanks, GATK is great!

Vivek

Post edited by Geraldine_VdAuwera on

Best Answer

  • ebanksebanks Broad Institute ✭✭✭✭
    Accepted Answer

    The heterozygosity is the probability that the allele for a single chromosome is non-reference (which in humans is 1/1000 for SNPs). So even for an "inbred human" you would still expect a variant on a given chromosome once every 1000 bases. It is not the probability that a diploid sample is heterozygous at a given position.

Answers

  • ebanksebanks Broad InstituteMember, Broadie, Dev ✭✭✭✭
    Accepted Answer

    The heterozygosity is the probability that the allele for a single chromosome is non-reference (which in humans is 1/1000 for SNPs). So even for an "inbred human" you would still expect a variant on a given chromosome once every 1000 bases. It is not the probability that a diploid sample is heterozygous at a given position.

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