I have list of few thousands snps name (RS*) and want to know their MAF.
I used the link http://genome.ucsc.edu/cgi-bin/hgTables
But i get errors that not all the SNPs are known.
This is why first I want to check which SNP exist in UCSC.
How can I do it? Is there a list of all known snps in the UCSC.
If there is such list that I can download, I will make a short code in phyton to compare my SNPs.
Thanks
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m321.k321 •
Here's a one-liner to get a list of UCSC SNP names:
$ mysql --user=genome --host=genome-mysql.cse.ucsc.edu -A -D hg19 -e 'SELECT name FROM snp138Common' | tail -n +2 > snp138CommonNames.txt
If you want positional data, etc. there are other fields available in the snp138common table schema.
For example, if you want to know the type of functional variant for a given SNP name, add the func field to the query:
$ mysql --user=genome --host=genome-mysql.cse.ucsc.edu -A -D hg19 -e 'SELECT name, func FROM snp138Common' | tail -n +2 > snp138CommonNamesAndVariantTypes.txt
Hi Asaf,
each time that i try to run this with all SNPs the chrome is crashing...
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m321.k321 •
solution: don't use chrome.
Or, more easily, use Ensembl BioMart. Use the short variation database, filter by a list of IDs and get the MAF as an attribute. No coding involved.
when you say "get the MAF as an attribute" - fo you mean the 1000 genomes global MAF (ALL)?
Because I understood that the UCSC is the most accurate database and the MAF there is the most accurate?
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m321.k321 •
Yes, the 1000 genomes MAF will be good.
The dbSNP data in UCSC and Ensembl all comes from the same place - one possible difference is that Ensembl carry out an extensive QC process to get rid of anything that looks dodgy, whereas I believe UCSC lift it directly.
Thanks.
Can I get more info of the snp? like name of the gene or intergenic? inside intron or exon?
:)
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m321.k321 •
I couldn't find gene name. can you help me to find this attribute? thanks
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m321.k321 •
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