Test-drive the GATK tools and Best Practices pipelines on Terra
Check out this blog post to learn how you can get started with GATK and try out the pipelines in preconfigured workspaces (with a user-friendly interface!) without having to install anything.
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?