Mercurial > repos > ryanmorin > nextgen_variant_identification
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author | ryanmorin |
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date | Wed, 12 Oct 2011 19:50:38 -0400 |
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children | 361d6506850a |
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Various Galaxy tools for running SNVMix and filtering/annotating the SNVMix output files Installation ------------ 1) Place these files in $GALAXY_HOME/tools 2) Modify your configuration files appropriately, for example, add the tools to $GALAXY_HOME/tool_conf.xml (under the NGS analysis section, create a "variant calling" section) 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