Coverage/Read Depth per SNP in 1000Genomes

Question

[Floris Brenk]

Hi all,

I want to use 1000Genomes as control population for a small case-case control study. Now I want to be sure that the genotypes from 1000Genomes are good so I wanted to know what the Coverage/Read Depth is for a few SNPs that I want to test. Is there an easy way to figure this out?

Any tips or hints are very welcome!

Answer 1

[lh3]

Check if you SNPs are present in one of the individual call sets here (e.g. si, ox or bc):

ftp://ftp-trace.ncbi.nih.gov/1000genomes/ftp/technical/working/20130723_phase3_wg/

They have read depth info in VCFs.

[Floris Brenk]

bc = ALL.chr4.bc.20130502.snps_indels_mnps_complex.genotypes.vcf.gz ox = ALL.chr4.oxford_platypus.20130502.snps_indels_mnps_cplx.low_coverage.genotypes.vcf.gz si = ALL.chrom4.samtools.20130502.snps_indels.low_coverage.genotypes.vcf.gz

So if the SNP is in there they are bad? I was hoping to filter variants on a read depth of 20 more or less..