Hi, I want to know information of allele frequency of each HapMap sample, but I didn't find the information, in spite of many trying. So I ask for any help about the issue.
I downloaded genotype file in HapMap site of my interest:
ALL.chip.omni_broad_sanger_combined.20140818.snps.genotypes.vcf.gz.
And I extracted information what I interested in and the result are shown in below.
CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA07014 NA10840
1 689186 rs4000335 G A . PASS AC=0;AF=0.00;AN=4282;set=broad GT ./. ./.
1 752566 rs3094315 G A . PASS AC=3422;AF=0.739;AN=4632;set=Intersection GT 1/1 1/1
1 752721 rs3131972 A G . PASS AC=3111;AF=0.673;AN=4626;set=Intersection GT 1/1 1/1
1 776546 rs12124819 A G . PASS AC=414;AF=0.092;AN=4480;set=Intersection GT 0/1 0/1
1 798959 rs11240777 G A . PASS AC=1805;AF=0.390;AN=4626;set=Intersection GT 0/0 1/0
1 800007 rs6681049 T C . PASS AC=4249;AF=0.926;AN=4590;set=Intersection GT 1/1 1/1
This file showed genotype of each HapMap sample (NA07014 and NA10840). In INFO column, AC and AF were shown, but I don't understand what meaning of the AC and AF is. I expected each AC and AF were shown in the vcf file.
So,
1) Does the values mean AC and AF of dbSNP? How the values were calculated?
2) And I want to know each AC and AF of each HapMap sample, How can I do it?
Thanks for any comment.
Soojin
