Filtering by specific genotype VCF
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?
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agata88
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virpatel3 •
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virpatel3 •
1 answer
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
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is it 274 vcf with one sample , or 1 vcf with 274 samples (and what should you do if only one sample is Het) ?
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.