VQSR on GENOTYPE_GIVEN_ALLELES mode

trgalltrgall Posts: 13Member

When using GENOTYPE_GIVEN_ALLELES with HaplotypeCaller, which uses EMIT_ALL_SITES and so has many calls where the entire cohort is nonvariant, do these reference only sites have to be filtered out before calling VQSR?

Tagged:

Answers

Sign In or Register to comment.