Attention: Want an end-to-end pipelining solution for GATK Best Practices?
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?