Pulling out all the SNPS listed in DBSNP from human exome

[ron128]

Heya everyone, is there any way i could pull out all the SNPS present in dbsnp 135 from the human exome? I have been trying to do thism but i am not well versed in SQL/ Database scripting. Any pointers would be really appreciated. I will break down the problem below:

1) Pull out all genes which constitute the human exome from hg 19 genome (this should be easy and I already have a gene list)

2) Find out which SNPS are present in these genes constituting the entire human exome.

What would i need for such an exercise? Would the gene hugo symbols/ entrez ids suffice or would i also need the start and end co ordinates? Also, is it advisable to do this in genes per se, or transcripts of these genes, as different transcripts might have different variants depending on the way they are spliced.

Thanks a lot!

[aeonsim]

One way not using the database is to download a dbsnp VCF file and then use bedtools to do a intersect with a bed or GTF file of human exomes.

[ron128]

Thanx a ton bro! will try this out and post the results soon! thanks a lot!

[billyziege]

Also, vcftools.

Just stumbled upon thread and wanted to point out that vcftools also has a flag that filters on bed files, i.e. --bed.

http://vcftools.sourceforge.net/options.html