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Decreasing heterozygosity parameter increases number of variants called


I am calling variants in exome resequencing of a sample of inbred barley lines using the HaplotypeCaller. Initially, I set the heterozygosity parameter to 0.008, which is the average coding sequence diversity (Tajima's pi) in cultivated barley. In the 60MB capture, I call about 500,000 single nucleotide variants, which seems appropriate given our previous information.

Our collaborators asked us to re-run the variant calling with the default parameters, to see what effect changing the heterozygosity parameter has. When I do, the HaplotypeCaller calls almost one million variants, over twice what we would expect.

Why would this be? Intuitively, I would expect that decreasing the heterozygosity parameter by almost an order of magnitude would under-call variants. Instead, it has the opposite effect.

I am using GATK 2.8-1. Thank you!

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