How To Calculate A Population Specific Allele Freq In 1000 Genomes Release 20101123 Using Vcftools?

Question

[Noel]

Hi all,

Following Lars question,

is there a way to calculate the population specific allele frequencies from the 20101123 1000 genome release using tabix and vcftools?

Currently I am just able to extract the genotypes with tabix for defined chromosomal regions and calculate their frequency with vcftools. However I know those frequencies are underestimated due to the mixture of populations·

I am running:

$ tabix -f -h ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20101123/interim_phase1_release/ALL.chr19.phase1.projectConsensus.genotypes.vcf.gz 19:53344800-53344900 > LIG1.vcf

$ vcftools --vcf LIG1.vcf --freq --out freq-LIG1

...as suggested by Stephen.

Thank you!!

Answer 1

[Raony Guimarães]

You could get the individuals from the population you want to calculate from this file :

ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20101123/interim_phase1_release/interim_phase1.20101123.ALL.panel

and calculate the frequencies with the command vcf-subset to get the genotypes only for this individuals:

Ex.

$tabix -f -h ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20101123/interim_phase1_release/ALL.chr19.phase1.projectConsensus.genotypes.vcf.gz 19:53344800-53344900 > LIG1.vcf

$vcf-subset -c NA0001,NA0002 LIG1.vcf > pop.LIG1.vcf

$vcftools --vcf pop.LIG1.vcf --freq --out freq-LIG1

[Noel]

Thanks a lot!

Noel