Filter heterozygous SNP calls out of a VCF file?

Question

[nute11a]

Hello,

I was wondering if there was a way to filter out heterozygous SNP calls from a VCF file. I am working with a model that has a doubled haploid genome, so we expect all calls to be homozygous, and any heterozygotes are a false positive which should be removed. Should I be filtering by genotype? Does anyone have any suggestions on how to do this?

Thank you!

[GenoMax]

Previous thread that may be useful: filter vcf file heterozygous calls by allelic depth

[Pierre Lindenbaum]

multi-samples ? what happens if only one sample is HET ? Input/output is needed.

Answer 1

[nute11a]

Hey! I figured it out -- sorry for the late response. I used GATK and did isHet and then set filtered genotypes to no call. Thank you for your help.