How To Retrieve Coding Snps Typed Only In 1000G Data

Question

[Sarah Tyrell]

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.

[Sean Davis]

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

[Giovanni M Dall'Olio]

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?

Answer 1

[Simon P]

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)