Hi,

I am working with a pre-exists mutation list in Granges, this data have some fields chr, position,ref, alt, strand, because our positions are limited to refgene, So I only want to annotation our mutations with:

1) mutations outcome in protein coding

2) mutations change spice sites

I know that here are a lots of tools can help to annotation, such as 'ANNOVA' and maftools, but them seems cant not accpect strand infomation and too heavy for my purpose.

I want to know are there other lightweight tools that can perform this analysis

Regrads

Zhang