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.
Increase max allowed compute PLs for an allele
When running GenotypeGVCFs (v3.7), I get a small number of sites (<100) that are not called because of:
DEBUG 13:35:31,518 ReferenceConfidenceVariantContextMerger - location chr21:44483184 has too many alleles (73) to compute PLs (maximum allowed 50). PL genotype annotations won't be produced at this site
WARN 13:35:31,550 GenotypingEngine - Attempting to genotype more than 50 alleles. Site will be skipped at location chr21:44483184
How do I increase this number? I have played around with --max_alternate_alleles, --max_genotype_count, and --max_num_PL_values with no luck.