Question: Coverage/Read Depth per SNP in 1000Genomes
gravatar for Floris Brenk
3.7 years ago by
Floris Brenk900
Floris Brenk900 wrote:

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!

snp coverage 1000genomes • 1.0k views
ADD COMMENTlink modified 3.7 years ago by lh331k • written 3.7 years ago by Floris Brenk900
gravatar for lh3
3.7 years ago by
United States
lh331k wrote:

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

They have read depth info in VCFs.

ADD COMMENTlink written 3.7 years ago by lh331k

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..

ADD REPLYlink written 3.7 years ago by Floris Brenk900
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: 1735 users visited in the last hour