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