Question: Help Parsing vcf for indels and splice sites
0
gravatar for Cece
3.9 years ago by
Cece0
United States/Houston
Cece0 wrote:

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...

snp • 1.3k views
ADD COMMENTlink modified 3.9 years ago by Ashutosh Pandey11k • written 3.9 years ago by Cece0
1
gravatar for Ashutosh Pandey
3.9 years ago by
Philadelphia
Ashutosh Pandey11k wrote:

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/

 

ADD COMMENTlink modified 3.9 years ago • written 3.9 years ago by Ashutosh Pandey11k
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