Question: retrieval of population specific SNPs
0
gravatar for 12021560-002
4.7 years ago by
12021560-00210
12021560-00210 wrote:

Hi! I have a list of SNPs and want to retrieve from this list the SNPs that are found in Asian population only. could you please tell me any software for this purpose.

ADD COMMENTlink modified 4.7 years ago by Denise CS5.1k • written 4.7 years ago by 12021560-00210

How long is your list? What format is it in?

1000 Genomes has the East Asian superpopulation and South Asian superpopulation. Are you interested in both of these or just one?

ADD REPLYlink modified 4.7 years ago • written 4.7 years ago by Emily_Ensembl21k

there are about 300 SNPs in the list and i want to filter this list for South Asian and East Asian population.

ADD REPLYlink written 4.7 years ago by 12021560-00210
1
gravatar for alexisdereeper
4.7 years ago by
alexisdereeper30 wrote:

Hi! You can use SNiPlay for this purpose, that allows to assign individuals to groups/populations and then compare SNPs and help to define specific/shared SNPs... The Fst analysis (diversity analysis) allows to get SNPs that discriminates between 2 pop (Fst=1) http://sniplay.southgreen.fr/cgi-bin/analysis_v3.cgi

ADD COMMENTlink written 4.7 years ago by alexisdereeper30
1
gravatar for Denise CS
4.7 years ago by
Denise CS5.1k
UK, Hinxton, EMBL-EBI
Denise CS5.1k wrote:

You can use the Ensembl VEP to find out the allele frequency for the Asian populations whether East (EAS) or South (SAS) from both 1000 Genomes and ExAC projects. The VEP accepts all sorts of input data (rsID, genomic locations, VCF, HGVS) and can be accessed online, via a Perl script or the Ensembl REST API. For the online interface for example simply explore the 'Frequency data' and 'Filter' fields to select which populations you want the frequency for.

ADD COMMENTlink written 4.7 years ago by Denise CS5.1k
0
gravatar for Matt Miossec
4.7 years ago by
Matt Miossec350
UK/Oxford/Wellcome Centre for human genetics
Matt Miossec350 wrote:

You'll want to use the Exome Aggregation Consortium (ExAC) Data Set: http://exac.broadinstitute.org/ to get the sub-population frequencies for all your SNPs. The frequencies are based on a very large data set (60,706 unrelated individuals). If you have the position, reference and variant allele for each of your SNPs, you can access the ExAC population frequencies using the web version of Annovar: http://wannovar.usc.edu/ all you need to do is arrange your list so that it is in the Annovar format.

If you don't have the position, reference and variant allele for each SNP, you can generate these using BioMart: http://www.ensembl.org/biomart/martview/

ADD COMMENTlink modified 4.7 years ago • written 4.7 years ago by Matt Miossec350
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