How to extract SNPs from vcf file based on Population

Question

[aadhirareddy1323]

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

Answer 1

[NB]

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

[aadhirareddy1323]

Thanks a ton Nandini ... it works :)

[padakanti.sridevi]

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 ?

[NB]

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

[aadhirareddy1323]

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