Question: Filtering by specific genotype VCF
0
gravatar for virpatel3
9 weeks 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 • 167 views
ADD COMMENTlink modified 10 days ago by agata88610 • written 9 weeks 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 9 weeks ago by Pierre Lindenbaum96k

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 9 weeks ago by virpatel320
0
gravatar for agata88
10 days ago by
agata88610
Poland
agata88610 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 10 days ago by agata88610
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