Does HaplotypeCaller allow multiple allele calls?
I'm trying to use HaplotypeCaller to call variants from a pooled population sample. However whenever I run the basic program, with the ploidy set to 2 x number of individuals in the pool, I get this warning;
WARN HaplotypeCallerGenotypingEngine - Removed alt alleles where ploidy is 88 and original allele count is 3, whereas after trimming the allele count becomes 2. Alleles kept are:[T*, A]
What is going on behind the scenes to reduce the allele count down to two? Is there a way to turn this off?