0
|
1 Various Galaxy tools for running SNVMix and filtering/annotating the SNVMix output files
|
|
2
|
|
3 Installation
|
|
4 ------------
|
|
5
|
|
6 1) Place these files in $GALAXY_HOME/tools
|
|
7 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)
|
|
8
|
|
9 Requirements
|
|
10 ------------
|
|
11 1) SNP list (can be user-provided), an example for hg18 is provided at the FTP site below
|
|
12 2) Codon-lookup table (used for annotation), an example based on Ensembl 54 and hg18 is also provided at the FTP site provided
|
|
13
|
|
14 ftp://ftp03.bcgsc.ca/public/rmorin/resources/
|
|
15 (also see README.txt in that directory)
|
|
16
|
|
17 3) SNVMix binary version 0.12.* or later (source can be downloaded at the link provided)
|
|
18 -follow installation instructions and put SNVMix2 binary in a location on the galaxy user's PATH
|
|
19
|
|
20 http://compbio.bccrc.ca/?page_id=204
|
|
21
|
|
22 Contacts:
|
|
23 Rodrigo Goya for problems with SNVMix2 binary
|
|
24 rgoya@bcgsc.ca
|
|
25
|
|
26 Ryan Morin for other problems
|
|
27 rmorin@bcgsc.ca
|
|
28
|