Question: Filtering by specific genotype VCF
0
gravatar for virpatel3
13 months ago by
virpatel320
United States
virpatel320 wrote:

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?

genotype filter vcf • 446 views
ADD COMMENTlink modified 11 months ago by agata88670 • written 13 months ago by virpatel320

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

ADD REPLYlink written 13 months ago by Pierre Lindenbaum110k

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.

ADD REPLYlink written 13 months ago by virpatel320
1
gravatar for agata88
11 months ago by
agata88670
Poland
agata88670 wrote:

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

ADD COMMENTlink written 11 months ago by agata88670
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