Help Parsing vcf for indels and splice sites

Question

[Cece]

Hi,

I'm trying to parse a dbSNP vcf file for information on the different validated mutations - missense, silent, indels, splice sites, etc. I've managed to get counts of the missense and nonsense using grep -c "NSM" filename but I can't figure out how dbSNP codes indels and splice sites or how to get at them. I've opened the vcf file to take a look at the descriptions but haven't made any progress. I 'm a total newbie to informatics so please bear with me. Are there tools out there to perform this task more proficiently or am I on the right path with grep, and how do I identify and locate my indels/ splice sites.

Answer 1

[Ashutosh Pandey]

• ASS - acceptor splice site
• DSS- donor splice site
• INDEL- insertions/deletions

See here for more information: http://www.ncbi.nlm.nih.gov/variation/docs/glossary/