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.