Question: Get Coding Snps For 1000 Genomes Data
1
gravatar for Korban
7.7 years ago by
Korban10
Korban10 wrote:

Edit. How can I get the coding SNPs (coding synonymous and non-synonymous polymorphisms) for a particular gene (say, BRCA1) from 1000 genomes data?

BioMart provides a nice interface to 1000 genomes data, but it just takes forever to output. Is there an alternative where I can simply look for the coding SNPs by providing the gene id or the corresponding genomic region?

Thanks

genome gene snp retrieval • 2.9k views
ADD COMMENTlink modified 4.4 years ago by Biostar ♦♦ 20 • written 7.7 years ago by Korban10

Why would you want to retrieve this from 1000 Genomes data rather than Ensembl? Do you want to retrieve reads mapping to a gene or the sequence itself?

ADD REPLYlink written 7.7 years ago by Daniel Swan13k

Hi Daniel, I want to check for the polymorphisms in a gene of interest.

ADD REPLYlink written 7.7 years ago by Korban10
2
gravatar for Karl
7.7 years ago by
Karl330
USA
Karl330 wrote:

To find polymorphisms in a gene of interest, I would get the gene's general region as chromosome and start/stop location (plus a kilobase or ten on each end for regulatory regions). Then go to Ensembl or Biomart or dbSNP and ask for known variants in that region.

ADD COMMENTlink written 7.7 years ago by Karl330

You can also search by gene name / symbol in Ensembl (e.g. 'BRCA2'). To get a list of the variants in a gene go to the 'Variant Table' page (e.g. http://www.ensembl.org/Homo_sapiens/Gene/Variation_Gene/Table?g=ENSG00000139618;r=13:32889611-32973805). You can configure the page using [Configure this page] in the side menu. Note that by default we show only variants that are located in the exons and up till 100 bp away from the exons. To see all intronic variants as well as the variants up to 5 kb up- and downstream of the gene, set 'Intron Context' on the configuration page to 'Full Introns'.

ADD REPLYlink written 7.7 years ago by Bert Overduin3.6k
1
gravatar for Prateek
7.7 years ago by
Prateek1.0k
Boston, MA
Prateek1.0k wrote:

You could use one of the SIFT tools to filter out non-coding variants. The name of the tool is "Restrict to coding variants" here is the link http://sift.bii.a-star.edu.sg/www/SIFT_intersect_coding_submit.html

Remember to choose the genome build and the input format. It can take in multiple formats like VCF4, pileup, MAQ or SIFT's own simple comma delimited formats.

ADD COMMENTlink written 7.7 years ago by Prateek1.0k
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