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author rdaveau
date Fri, 03 Aug 2012 05:50:41 -0400
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## What is gfap ?
The Genomic and Functional Annotation Pipeline (gfap) consists in a set of perl and R tools that
aim at annotating human genetic SNVs/InDels identified by 2nd-generation sequencing technologies.

## How does it work ?
gfap starts with a samtools-formatted VCF-file i.e. the DP4-tag from the INFO field is mandatory.
gfap performs its annotation in a 4-steps linear procedure i.e.:
1> SAMVCF.data.parser 2> Known.variants.finder 3> Map.to.genomic.features 4> Map.to.dbNSFP.features

## Pre-requisites
In gfap_r1.0_samvcf_data_parser.pl LINE 13 the $rbin assumes that your R binary is set to /usr/bin/R
So, you will have to properly edit and reset this $rbin if R is installed elsewhere on your system.