Annotation of SNPs

[mgibson]

Sorry if this is a really obvious question - I feel like there has to be an easy answer that I am just overlooking. I've used SAMtools mpileup to call SNPs in my RNAseq data. The SNPs are then listed by chromosome and position. How do annotate them so that the gene and whether they are intronic or exonic is matched with the SNP?

Thanks for any help you all can give me!

[zee]

Wise enough not to reinvent the wheel and try the following tools:

snpEff http://snpeff.sourceforge.net/
annovar http://www.openbioinformatics.org/annovar/


snpEff has a larger choice of reference annotation databases and supports the pileup format. It also supports VCF format.

Sorry if this is a really obvious question - I feel like there has to be an easy answer that I am just overlooking. I've used SAMtools mpileup to call SNPs in my RNAseq data. The SNPs are then listed by chromosome and position. How do annotate them so that the gene and whether they are intronic or exonic is matched with the SNP?

Thanks for any help you all can give me!