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.

Best Answer

Answers

Sign In or Register to comment.