Identify SNPs of selected genes in VCF file from DGRP

Question

[mufernando]

Hi,

I'm starting to work with Drosophila genomics, but I don't have a clue of where to start.

I wanted to identify the possible SNPs of a few genes from the VCF that you can find in the DGRP. I tried to do this in the genome browser, but there isn't the SNP section in Variation, and so the only possible way to do this is by analysing the VCF.

Could somebody give me some directions of where to start?

Answer 1

[Darked89]

You need to intersect SNP data in a VCF file with some genomic position data for your genes of interest stored as either BED or GFF. Start small with one gene or 1kb genomic interval using i.e. "bedtools intersect"

http://bedtools.readthedocs.org/

[mufernando]

I forgot to thank you Darked89! this was very helpful.