Question: Genotype quality scores in 1000 Genomes vcf files
gravatar for eric.letouze
5.7 years ago by
eric.letouze0 wrote:


I have downloaded the release 3 of 1000 Genomes data on their ftp server.

I would like to apply quality thresholds to keep only SNPs with a good coverage and calling quality for each sample.

However the genotype field only contains the genotype itself, without information on read depth and genotype quality.

Does anyone know where I can find these data?

Thank you very much in advance,


snp • 1.7k views
ADD COMMENTlink modified 5.7 years ago by ngsgene350 • written 5.7 years ago by eric.letouze0
gravatar for ngsgene
5.7 years ago by
United States
ngsgene350 wrote:

What are your criteria for good calling quality? One option could be to check out their vcf files or generate PLINK files using genotype data and then generating summary statistics. Have included some links:

Qual Scores In 1000 Genomes Vcf File

ADD COMMENTlink modified 5.7 years ago • written 5.7 years ago by ngsgene350
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1038 users visited in the last hour