Question: How To Retrieve Coding Snps Typed Only In 1000G Data
2
gravatar for Sarah Tyrell
9.3 years ago by
Sarah Tyrell20
Sarah Tyrell20 wrote:

Good afternoon,

I have a list of 100 genes for which (in fact, for one of their transcripts in particular) I would like to get "synonymous coding" and "non-synonymous coding" SNPs that are observed in 1000G data (n=629).

Moreover, it would be fantastic to somehow extract the heterozygosity status for those SNPs.

I tried the ENSEMBLE 1000G browser, however, there are inconsistencies, that is, some SNPs that appear in the VCF file do not show up in the browser view. In addition, I do not want to mess with the dbSNP but am only interested in the SNPs observed in 1000G.

Any help would be much appreciated.

genome non snp • 2.5k views
ADD COMMENTlink modified 6 months ago by Biostar ♦♦ 20 • written 9.3 years ago by Sarah Tyrell20

Do you have the VCF file describing the 1000G variants that you want to use?

ADD REPLYlink written 9.3 years ago by Sean Davis26k

The inconsistencies you see are probably caused by the fact that there are different 1000genomes releases. In particular, they have published a new one in October 2011, including almost 2000 individuals (http://www.1000genomes.org/announcements/october-2011-integrated-variant-set-release-ichg2011-2011-10-12). Which release are you interested to?

ADD REPLYlink modified 14 months ago by _r_am31k • written 9.1 years ago by Giovanni M Dall'Olio27k
1
gravatar for Simon P
9.1 years ago by
Simon P10
Simon P10 wrote:

Sarah,

A pretty direct pipeline should allow you to do so.

  1. Get the chromosomal coordinates of your genes

  2. Extract the SNPs contained in the regions found in 1 (make sure that you use the same genome annotation version)

  3. Use a variant annotation software to annotate the SNPs (IE : ANNOVAR)
ADD COMMENTlink modified 9.1 years ago by Giovanni M Dall'Olio27k • written 9.1 years ago by Simon P10
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