Question: Where is Information of allele frequency of each HapMap sample?
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gravatar for Lucy
14 months ago by
Lucy 0
Korea, Republic Of
Lucy 0 wrote:

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

snp • 403 views
ADD COMMENTlink written 14 months ago by Lucy 0
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