Mercurial > repos > rdaveau > gfap
diff gfapts/README @ 0:f753b30013e6 draft
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author | rdaveau |
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date | Fri, 29 Jun 2012 10:20:55 -0400 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/gfapts/README Fri Jun 29 10:20:55 2012 -0400 @@ -0,0 +1,12 @@ +## 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. \ No newline at end of file