Tagged with #pooled calls
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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

There are 4 comments on this article. To see them or add your own, read this post on the forum

There are 3 comments on this article. To see them or add your own, read this post on the forum

Hi to all,

There are 3 comments on this article. To see them or add your own, read this post on the forum

There are 2 comments on this article. To see them or add your own, read this post on the forum

Thank you for developing a great set of tools and adding in the ploidy option to the UnifiedGenotyper! My question is in regards to the ploidy argument when calling multiple pooled samples together. If I have pooled samples from the same population at different time points and want to call SNPs with multiple sample awareness, do I use the ploidy of one sample or that of all samples. For example, if I have pooled samples of approximately 25 haploid genomes each from three different time points from the same population should I use 25 or 75 as my ploidy?

There are 2 comments on this article. To see them or add your own, read this post on the forum