Question: Filtering by specific genotype VCF
gravatar for virpatel3
4 months ago by
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 • 225 views
ADD COMMENTlink modified 9 weeks ago by agata88610 • written 4 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 4 months ago by Pierre Lindenbaum99k

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 3 months ago by virpatel320
gravatar for agata88
9 weeks ago by
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?



ADD COMMENTlink written 9 weeks ago by agata88610
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