masking vcf for brain expressed variants

[willMD]

I would like to look at my whole genome vcf for variants that are likely expressed in brain. I see that the IGV server has Body Map brain coverage and bam tracks available. Can I use bedtools somehow to use the Body Map transcriptome data to select only the genome variants that are expressed in brain? It seems to me to be a masking function rather than intersect function. Any suggestions on easy ways to accomplish this?

-Will in Maryland

[swbarnes2]

You've got two general approaches; annotate all your SNPS, and then filter by the gene name, or get a list of positions of where the genes you care about are, and then BEDTools can filter your vcf for SNPs that fall in those positions.