Filter heterozygous SNP calls out of a VCF file?
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!
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Previous thread that may be useful: filter vcf file heterozygous calls by allelic depth
multi-samples ? what happens if only one sample is HET ? Input/output is needed.