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.
Biallelic variants only with HaplotypeCaller
I want to restrict the
HaplotypeCaller to only call biallelic sites. I'm thinking that this can be accomplished with
--max_alternate_alleles, although I'm not 100% whether this parameter should be set to 1 or 2 (one alternate allele, or two different alleles?).
--max_genotype_count seems relevant here also, but I don't understand what it does.
Basically, how do I ensure calling only biallelic sites?