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Adjusting priors for heterozygosity for pooled samples in UnifiedGenotyper

jdavilajdavila Posts: 4Member

Hi to all,

I am calling variants in a pooled sample of 3 human samples, using UnifiedGenotyper and a ploidy of 6 and I was wondering if it is necessary to adjust the heterozygosity rate (--heterozygosity) to be 0.003 instead of the default of 0.001, or if the model used in the pooled sample calling already takes this into account.Thanks a lot,

Jaime

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  • jdavilajdavila Posts: 4Member

    Eric

    Sorry for not being more clear in my earlier post. I am running UnifiedGenotyper multi-sample calling on several samples (say 20). Each one of the samples is a pool of three individuals without barcoding or multiplexing, hence I am using ploidy of 6. Are you saying that even when I have pooled individuals in a sample I need not change the heterozygosity rate? I was thinking that since each "sample" is a combination of three individuals the chances of a heterozygous call go up by three.

    Thanks a lot for your detailed answer,

    Jaime

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