This is a test version of Biostars. For the public version, visit https://www.biostars.org.
How to check if my SNPs are also present in 1000 genome project

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

1000genomes snp
• 2,584 views • link
updated by Ram Ram • written by Dataminer Dataminer

2 answers

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.

• 2 views • link
updated by Ram Ram • written by Pierre Lindenbaum Pierre Lindenbaum

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!

• 0 views • link
written by Ram Ram

Log in to answer this question.

More posts like this