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Hi all --
I'm trying to decide on a heterozygosity parameter to use with the GATK UnifiedGenotyper. I'd be interested to know how other people have computed or chosen a value. I'm working in dog, so there are some factors related to artificial selection and others about having fewer resources to consult than mouse or human.
Here's what GATK has to say about it:
--heterozygosity / -hets (Double with default value 0.0010)
Heterozygosity value used to compute prior likelihoods for any locus. The expected heterozygosity value used to compute prior likelihoods for any locus. The default priors are: het = 1e-3, P(hom-ref genotype) = 1 - 3 * het / 2, P(het genotype) = het, P(hom-var genotype) = het / 2
Thanks!
I'm trying to decide on a heterozygosity parameter to use with the GATK UnifiedGenotyper. I'd be interested to know how other people have computed or chosen a value. I'm working in dog, so there are some factors related to artificial selection and others about having fewer resources to consult than mouse or human.
Here's what GATK has to say about it:
--heterozygosity / -hets (Double with default value 0.0010)
Heterozygosity value used to compute prior likelihoods for any locus. The expected heterozygosity value used to compute prior likelihoods for any locus. The default priors are: het = 1e-3, P(hom-ref genotype) = 1 - 3 * het / 2, P(het genotype) = het, P(hom-var genotype) = het / 2
Thanks!