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
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
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.
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
Hope this helps!