Genotype quality scores in 1000 Genomes vcf files

Question

[eric.letouze]

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

Answer 1

[ngsgene]

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