Get Snps For A List Of Gene Symbols In A Text File As A Single Column

Question

[confusedious]

Hello everyone,

I have assembled a list of all genes (~1744) that fall within a GO category of interest and would like to assemble a list of SNPs that fall within these genes. I have previously used an R package for this, but have found that this particular function doesn't work any longer (I'm guessing something has changed at the NCBI end and they aren't understanding one another anymore).

I have the list of gene symbols in a text file as a single column.

Does anyone know a quick and easy way to do this? I am sure there is one!

I would like to avoid scripting if at all possible, I am only familiar with R and even then only at a very elementary level.

Thank you for any help you might be able to offer.

Answer 1

[Pierre Lindenbaum]

You could use the UCSC mysql server:

$ echo -e "EIF4G1\nEIF4G2" |\
    awk 'BEGIN {printf("select distinct R.name,R.chrom,R.chromStart,R.chromEnd,X.geneSymbol from (snp137 as R,knownGene as G, kgXref as X ) where R.chrom=G.chrom and NOT(R.chromStart>=G.txEnd or R.chromEnd<=G.txStart) and X.kgId=G.name and X.geneSymbol in (\"-9999\"");} {printf(",\"%s\"",$0);} END {printf(");\n");}' |\
    mysql --user=genome --host=genome-mysql.cse.ucsc.edu -A -D hg19

or the ucsc tables

or

biomart

or

extract and grep the field GENEINFO in the NCBI VCFs

etc...

[confusedious]

I figured out how to do it BioMart - thank you.