Tagged with #pooled calls
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I using the UnifiedGenotyper to call SNPs in a pooled sample of 30 diploid individuals (i.e., I am setting the ploidy to 60). Does this mean that if the coverage is < 60 at a given variant site, the vcf file will read "./." for all alleles at that site? In other words, does it require the coverage to be >= the ploidy or it won't produce a called variant at that site? I'm just trying to make sure I am interpreting the vcf file correctly, in that: if there is a called genotype at a given variant site that I can interpret that as the estimated allele frequency in that pool.

Thanks in advance for any advice.

Best, Jon

Comments (2)

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?

Comments (4)

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