To celebrate the release of GATK 4.0, we are giving away free credits for running the GATK4 Best Practices pipelines in FireCloud, our secure online analysis portal. It’s first come first serve, so sign up now to claim your free credits worth $250. Sponsored by Google Cloud. Learn more at https://software.broadinstitute.org/firecloud/documentation/freecredits

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.