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I'm trying to run HaplotypeCaller on a haploid organism. Is this possible? What argument should I use for this?
My first attempt produced a diploid calls.
RoddyP
Posts: 1Member ✭
Answers
Currently the HaplotypeCaller only supports diploid calling. If you want to call non-diploid samples you'll need to use the UnifiedGenotyper.
Geraldine Van der Auwera, PhD
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