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Question: How to check if my SNPs are also present in 1000 genome project
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gravatar for Dataminer
5.7 years ago by
Dataminer • 2.7k
Netherlands
Dataminer • 2.7k wrote:

Hi!

 

I have a list of SNPs, how can I know which one of them are also present in 1000 genome project.

I cannot do this manually, their has to be an automated way, to upload the whole set of SNPs and check it out.

Thank you

 
snp 1000genomes • 1.6k views
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modified 5.7 years ago by Pierre Lindenbaum ♦ 128k • written 5.7 years ago by Dataminer • 2.7k
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gravatar for Pierre Lindenbaum
5.7 years ago by
Pierre Lindenbaum ♦ 128k
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum ♦ 128k wrote:

sort your SNPs

search dbsnp for `"1000genomes"[Submitter Handle]` ( http://www.ncbi.nlm.nih.gov/snp?term=%221000genomes%22[Submitter%20Handle] ) . Save as rs#id  and sort

use `comm` to get the common snps.

 
ADD COMMENT • link modified 5.7 years ago • written 5.7 years ago by Pierre Lindenbaum ♦ 128k
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gravatar for RamRS
5.7 years ago by
RamRS ♦ 27k
Houston, TX
RamRS ♦ 27k wrote:

I'd suggest using UCSC genome Browser's MySQL provisions and SQL queries.

How to connect to UCSC Genome Broser MySQL: https://genome.ucsc.edu/goldenPath/help/mysql.html

Table Schema: http://genome.ucsc.edu/cgi-bin/hgTables?db=hg19&hgta_group=varRep&hgta_track=tgpPhase1&hgta_table=tgpPhase1&hgta_doSchema=describe+table+schema

Hope this helps!
ADD COMMENT • link written 5.7 years ago by RamRS ♦ 27k
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