Question: How to extract SNPs from vcf file based on Population
0
gravatar for aadhirareddy1323
19 months ago by
aadhirareddy132330 wrote:

Dear Friends,

My vcf file has SNPs available for different population(Africa, America, Europe,East Asia and South Asia ). I want to extract the data for Europe and East Asia together . Kindly let me know the possible ways.

Thanks in Advance

linux 1000genomes vcf • 1.6k views
ADD COMMENTlink modified 8 months ago by zx87547.9k • written 19 months ago by aadhirareddy132330
3
gravatar for Nandini
19 months ago by
Nandini820
London
Nandini820 wrote:

You can do this easily using vcftools, GATK tools, plinkseq etc.

you first have to generate a text file with the list of samples that form the population of your choice, let's say "population_of_interest.txt" Then,

vcf-subset -e -c population_of_interest.txt input.vcf > output.vcf

or

vcftools --vcf input.vcf --keep population_of_interest.txt  --recode > output.vcf
ADD COMMENTlink written 19 months ago by Nandini820

Thanks a ton Nandini ... it works :)

ADD REPLYlink written 19 months ago by aadhirareddy132330

This code works fine when i run for one chromosome at a time. But, I want to extract SNPs for all chromosomes together ,please let me know if ithere is any other option ?

ADD REPLYlink written 6 months ago by padakanti.sridevi0

It should work for all chromosomes. Does your vcf input file have all chromosomes ?

ADD REPLYlink written 6 months ago by Nandini820

@Nandini .. I have VCF file for each chromosome seperately

ADD REPLYlink written 5 months ago by aadhirareddy132330
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