masking vcf for brain expressed variants

willMD

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Join Date: Mar 2013

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#1

masking vcf for brain expressed variants

07-09-2013, 10:18 AM

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
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swbarnes2

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Join Date: May 2008

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07-09-2013, 10:57 AM

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.
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