From b1fa83a9c6b47bb2032d8faf3801b48534881b1f Mon Sep 17 00:00:00 2001 From: Yoann Pradat Date: Thu, 13 Aug 2020 18:41:36 +0200 Subject: [PATCH] update README with install details --- README.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/README.md b/README.md index 620513f..2851195 100644 --- a/README.md +++ b/README.md @@ -51,11 +51,11 @@ perl INSTALL.pl The perl script INSTALL.pl may return errors as missing dependencies or other. For instance,the error `Bio::Root::Version is not installed` may be solved by running `sudo cpanm Bio::Root::Version`. You may have more than one such library to install. Refer to the github for the details. -The installation from the perl script offers the choice to install cache files (most efficient use of vep) and FASTA files (to retrieve sequence data for HGVS notations) into `$HOME/.vep`. You may also install plugins for additional analyses. Download cache files for Homo Sapiens genome 99_GRCh37 (or newer). The total download size is about 12 GB of data so a stable and fast connection is required here. The FASTA file Homo_sapiens.GRCh37.75.dna.primary_assembly.fa.gz requires 882 MB of storage. *DO NOT FORGET* to unzip this file (or VEP will fail). +The installation from the perl script offers the choice to install cache files (most efficient use of vep) and FASTA files (to retrieve sequence data for HGVS notations) into `$HOME/.vep`. You may also install plugins for additional analyses. Download cache files for Homo Sapiens genome 100_GRCh37 (or newer). The total download size is about 12 GB of data so a stable and fast connection is required here. The uncompressed FASTA file (**DO NOT FORGET** to uncompress this file or VEP will fail) Homo_sapiens.GRCh37.75.dna.primary_assembly.fa.gz requires about 3.0 GB of storage. ### 2.2 Install vcf2maf -VEP is required by vcf2maf may you need also need the set of commands `samtools`, and `htslib` available at [http://www.htslib.org/download/](http://www.htslib.org/download/). Do the following +VEP is required by vcf2maf but you also need the commands from `samtools` and `htslib` available at [http://www.htslib.org/download/](http://www.htslib.org/download/). Do the following ``` cd samtools-1.x -- GitLab