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What if Ploidy is set to 2 for pooled DNA sequencing experiment?
I performed a pooled sequencing experiment with 60 individuals and am trying to call variants using HaplotypeCaller. The ploidy is technically supposed to be set at 120. But there are known issues with high ploidy and HC not designed to handle it. Since this is a pooled experiment, I can only get allele frequency and not individual level variants anyways. Furthermore I am not interested in rare alleles either.
So what if I set the ploidy to 2 (and maxAltalleles to 3 or 4 )? For the program, would it appear that that the reads are actually coming from a diploid individual sequenced at high depth?
Please let me know.