Mercurial > repos > ryanmorin > nextgen_variant_identification
view SNV/README @ 7:351b3acadd17 default tip
Uploaded
author | ryanmorin |
---|---|
date | Tue, 18 Oct 2011 18:33:15 -0400 |
parents | 361d6506850a |
children |
line wrap: on
line source
Various Galaxy tools for running SNVMix and filtering/annotating the SNVMix output files Installation ------------ 1) Place these files in $GALAXY_HOME/tools and compile/install SNVMix2 if you haven't already done so (also copy/link the SNVMix2 binary, identify_nonsynonymous_mutations.pl and filter_snvmix.pl to /usr/local/bin or some other location in the default PATH, also ensure they are executable) 2) Modify your configuration files appropriately -add the tools to $GALAXY_HOME/tool_conf.xml (under the NGS analysis section, create a "variant calling" section), see the tool_conf.xml.sample for an example -create or modify $GALAXY_HOME/sam_fa_indices.loc to match the example provided (points galaxy to the fasta files containing the genome that was used during the alignment step). These are needed by SNVMix. Requirements ------------ 1) SNP list (can be user-provided), an example for hg18 is provided at the FTP site below 2) Codon-lookup table (used for annotation), an example based on Ensembl 54 and hg18 is also provided at the FTP site provided ftp://ftp03.bcgsc.ca/public/rmorin/resources/ (also see README.txt in that directory) 3) SNVMix binary version 0.12.* or later (source can be downloaded at the link provided) -follow installation instructions and put SNVMix2 binary in a location on the galaxy user's PATH http://compbio.bccrc.ca/?page_id=204 Contacts: Rodrigo Goya for problems with SNVMix2 binary rgoya@bcgsc.ca Ryan Morin for other problems rmorin@bcgsc.ca