Mercurial > repos > ryanmorin > nextgen_variant_identification
diff SNV/README @ 0:74f5ea818cea
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| author | ryanmorin |
|---|---|
| date | Wed, 12 Oct 2011 19:50:38 -0400 |
| parents | |
| children | 361d6506850a |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/SNV/README Wed Oct 12 19:50:38 2011 -0400 @@ -0,0 +1,28 @@ +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 +