Question: Coverage/Read Depth per SNP in 1000Genomes
1
gravatar for Floris Brenk
3.0 years ago by
Floris Brenk890
USA
Floris Brenk890 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 • 873 views
ADD COMMENTlink modified 3.0 years ago by lh331k • written 3.0 years ago by Floris Brenk890
0
gravatar for lh3
3.0 years ago by
lh331k
United States
lh331k wrote:

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.

ADD COMMENTlink written 3.0 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 3.0 years ago by Floris Brenk890
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