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author rdaveau
date Fri, 03 Aug 2012 05:50:41 -0400
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1 ## What is gfap ?
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2 The Genomic and Functional Annotation Pipeline (gfap) consists in a set of perl and R tools that
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3 aim at annotating human genetic SNVs/InDels identified by 2nd-generation sequencing technologies.
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5 ## How does it work ?
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6 gfap starts with a samtools-formatted VCF-file i.e. the DP4-tag from the INFO field is mandatory.
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7 gfap performs its annotation in a 4-steps linear procedure i.e.:
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8 1> SAMVCF.data.parser 2> Known.variants.finder 3> Map.to.genomic.features 4> Map.to.dbNSFP.features
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10 ## Pre-requisites
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11 In gfap_r1.0_samvcf_data_parser.pl LINE 13 the $rbin assumes that your R binary is set to /usr/bin/R
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12 So, you will have to properly edit and reset this $rbin if R is installed elsewhere on your system.