This post is about Consequences, a tool finding the consequences of a set of mutations mapped on the human genome. It was motivated by a recent post of FriendFeed, Daniel MacArthur asked:“Given a list of human b36 coordinates for a list of genic SNPs (most not in dbSNP), what would be the quickest way to get a list of the genes they're found in and, if possible, the amino acid position they would affect?”.
About one year ago, I wrote a tool named "Consequences" answering this question but the sources are somewhere in a tar.gz , burned in an old CD, in a cardboard, in my cellar... so it was faster to re-write this simple code from scratch. The result should be fine but please, tell me if you find a bug.
This tool takes as input a tab delimited file containing the following fields:
- A Name for your SNP
- the chromosome e.g. 'chr2' (at this time only one chromosome per input is supported)
- the position on the chromosome. The first base is indexed at 0
- The base observed ON THE PLUS STRAND OF THE GENOME
The source code is available here:
A 'jar' is available for download at http://lindenb.googlecode.com/files/consequences.jar.
Running the tool:
Well, that is not big science but it might be helpful.