Question: Genotype quality scores in 1000 Genomes vcf files
0
gravatar for eric.letouze
4.8 years ago by
France
eric.letouze0 wrote:

Hi,

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,

Eric

snp • 1.6k views
ADD COMMENTlink modified 4.8 years ago by ngsgene350 • written 4.8 years ago by eric.letouze0
0
gravatar for ngsgene
4.8 years ago by
ngsgene350
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

http://www.1000genomes.org/node/101

http://pngu.mgh.harvard.edu/~purcell/plink/summary.shtml#mishap

ADD COMMENTlink modified 4.8 years ago • written 4.8 years ago by ngsgene350
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