Previously, when I needed to find a genomic feature (promoter, CDS, repeat etc) that underwent mutation (SNP) I used my own scripts to load an annotation file, parse it, map the SNP's position and output the sequence of the feature. Now that I'm moving from microbes to mammals with huge annotations, introns/exons and huge genomes, my scripts don't work that well and I'm sort of lazy to optimize the code or rewrite it in a faster language, since I'm sure there should be some prominent tools for the task. That's it, could you recommend me some tools that do the following:
- Given a reference genome, annotation and a VCF (or similar variant file) match the SNPs to genomic features in the annotation
- Output the entire feature that underwent mutation, e.g. if the SNP happened in a protein-coding gene, I need to have the entire protein-coding sequence not just an exon/intron.
Thanks in advance.