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.

Order of reporting sites by GenotypeGVCFS

KrzysztofMKozakKrzysztofMKozak Cambridge, UKMember

Hello,

When I genotype a large and diverse cohort I often see an error about too many alleles at one position, which is fine. What puzzles me is why the sites in question are not reported in order, e.g. here position 102k is highlighted after 501k:

INFO 20:56:15,037 ProgressMeter - 0101:9012801 0.0 30.0 s 50.1 w 2.4% 21.2 m 20.7 m
WARN 20:56:26,448 GenotypingEngine - Attempting to genotype more than 50 alleles. Site will be skipped at location 0101:5019574
WARN 20:56:43,879 GenotypingEngine - Attempting to genotype more than 50 alleles. Site will be skipped at location 0101:1023160

As far as I can tell the sites are ordered in the gVCFs. Is this an unimportant idiosyncrasy of the Progress Meter output, or does it point to a problem with my input files?

Many thanks,

Best Answer

Answers

Sign In or Register to comment.