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harvardinformatics / snpArcher

Snakemake workflow for highly parallel variant calling designed for ease-of-use in non-model organisms.
MIT License
63 stars 30 forks source link

Are genotype likelihoods available? #156

Closed Erythroxylum closed 4 months ago

Erythroxylum commented 4 months ago

Hello, Just a question for you all. Are the genotype likelihoods calculated by HaplotypeCaller accessible somewhere in the output? Thanks, Dawson

tsackton commented 4 months ago

The output is just a normal VCF file. Genotype likelihoods are in the PL format field.