Question: How Can I Overlay My Snp Variants With Various Databases
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gravatar for Nandini
6.5 years ago by
Nandini830
London
Nandini830 wrote:

Hello,

Has anyone tried to overlay human genomes variants with the 1000G or Hapmap or dbsnp. If so, what are the results like ?

For my human genomes, I tried to overlay using vcftools-

1) the solid data ( 3.2 million SNPs) with Hapmap (ftp://ftp.broadinstitute.org/bundle/2.3/hg19/hapmap_3.3.hg19.vcf ) :This gives me approx 22% overlay

2) the same sample sequenced with illumina (4.1 million SNPs) with Hapmap gives me 23%

Similarly, with dbsnp I get 54% for solid and 63% with illumina.

I am not sure if these results look good or I'm going wrong somewhere with my analysis.

Thank you.

hapmap 1000genomes dbsnp • 1.5k views
ADD COMMENTlink modified 6.4 years ago by ajc8120 • written 6.5 years ago by Nandini830
0
gravatar for ajc8
6.4 years ago by
ajc8120
University of Iowa
ajc8120 wrote:

Can you clarify what you mean by overlay? Is your goal to annotate variants with information from databases of known variants?

ADD COMMENTlink written 6.4 years ago by ajc8120

by overlay, I mean, I wish to see how many of my variants are present (or in common) with Hapmap or 1000genomes.

ADD REPLYlink written 6.3 years ago by Nandini830
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