Thanks a ton Nandini ... it works :)
• 0 views
•
link
written
by
aadhirareddy1323 •
How to extract SNPs from vcf file based on Population
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
• 6,064 views
•
link
updated
by
zx8754
•
written
by
aadhirareddy1323 •
•
written
by
aadhirareddy1323 •
1 answer
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
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 ?
• 1 views
•
link
written
by
padakanti.sridevi •
@Nandini .. I have VCF file for each chromosome seperately
• 0 views
•
link
written
by
aadhirareddy1323 •
Log in to answer this question.
More posts like this
-
Non-coding region of WGS
written by FL512 •
-
Crystal structure of lambda phage?
written by DanielC
-
Decipher VCF file similar to 1000 Genomes
written by aadhirareddy1323 •
-
Code to select randomly 1 SNP per scaffold
written by angelaparody •
-
Extract SNPs and SNP ID's from vcf file
written by aadhirareddy1323 •
-
How to convert VCF file into a binary matrix to find the genotype markers
written by aadhirareddy1323 •
-
How can get MAF for set of SNPs from each population based on 1000 Genome?
written by star
-
Can I apply ihs/ehh on snp?
written by evo_genomics •
-
Ancestral allele in VCF files
written by thjnant
-
How To Code Multiple States For Discrete Data Type
written by qiyunzhu
