Filtering by specific genotype VCF

Question

[virpatel3]

I have a vcf file with 274 samples in which I need to remove all heterozygotic SNPs for individual samples, since I am studying a haploid model. How can I best accomplish this?

[Pierre Lindenbaum]

is it 274 vcf with one sample , or 1 vcf with 274 samples (and what should you do if only one sample is Het) ?

[virpatel3]

So 274 samples in 1 VCF. If there is a heterozygous site, I'd like to remove it, with the distinction of ./. as is typically prescribed for sites without data. You see, this is genotype data for a malaria strain, which is haploid.

Answer 1

[agata88]

Hi! I found post in biostar that might be helpful. filter my vcf for heterozygous

To be curious, why do you have hetero variants if your organism is haploid?

Best,

Agata