[BioC] overlap GRangesList and vcf

Georg Otto gwo at well.ox.ac.uk
Fri Aug 10 18:55:54 CEST 2012


I apologise if this is trivial, but I haven't found a straight forward
way to do this so far.

Given a GRangesList with exons

## exons by gene
range.exon <- exonsBy(txdb.ensgene, "gene")

and a vcf file with SNP data (positions, alleles, etc), how can I
generate a list of exons that contain SNPs (along with SNP positions)?

Any hint will be appreciated!


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