Mercurial > repos > rdaveau > gfap
comparison 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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| -1:000000000000 | 0:f753b30013e6 |
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| 1 ## What is gfap ? | |
| 2 The Genomic and Functional Annotation Pipeline (gfap) consists in a set of perl and R tools that | |
| 3 aim at annotating human genetic SNVs/InDels identified by 2nd-generation sequencing technologies. | |
| 4 | |
| 5 ## How does it work ? | |
| 6 gfap starts with a samtools-formatted VCF-file i.e. the DP4-tag from the INFO field is mandatory. | |
| 7 gfap performs its annotation in a 4-steps linear procedure i.e.: | |
| 8 1> SAMVCF.data.parser 2> Known.variants.finder 3> Map.to.genomic.features 4> Map.to.dbNSFP.features | |
| 9 | |
| 10 ## Pre-requisites | |
| 11 In gfap_r1.0_samvcf_data_parser.pl LINE 13 the $rbin assumes that your R binary is set to /usr/bin/R | |
| 12 So, you will have to properly edit and reset this $rbin if R is installed elsewhere on your system. |