soft_exam

Resume :

ExAM is a 5 stages python tool to analyze exome sequencing data. First stage, it reads VCF files and annotates it using Annovar. Second stage, it filters the variants according to their quality, the consistency with the chosen genetic disease model and frequency constraint (e.g. absence) in public control databases. Third stage, it annotates the 2nd stage selected variants with an exhaustive set of relevant information, such as the genes summary function (from RefSeq2), their pathways (from Gene Ontology3, Biosystem4, KEGG5…)... Fourth stage it ranks variants according to the collected data and user provided keywords. Last stages, it provides information on all the analyzed samples; variant occurrence number, number of variant on a given gene and it allows the comparison of sample results by crossing the results by sample or phenotype.

• Download link - [Doc] (http://sourceforge.net/projects/exam-exome-analysis-and-mining/files/ExAM-1.5_Documentation.pdf/download)
• INPUTS : VCF
• OUTPUTS : -
• OS : Linux
• Techno : C, python 2, Java 1.7, MySQL 5.5

Pros:

Cons : Documentation hard to find, no website, ... just an python script alone in web Hard to install - lot of (and sometime old) dependencies, compilation error, ... Expert tool - lot of mandatory parameter All done client side - lot of mandatory parameter

Screenshots