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1 Installs VirtualNormal Correction Tool
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2
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3 After installing this tool via admin panel, manually configure the following:
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4
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5 1) edit virtual_normal_correction.loc file
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6
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7 - change "/path/to/hg18.crr" to the location of the Complete Genomics reference crr file on your system
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8 (can be downloaded from ftp://ftp.completegenomics.com/ReferenceFiles/ )
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9
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10 - change "/path/to/VN_genomes_varfiles_lists_hg18" to the location of the directory containing files with the locations of all the Complete Genomics
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11 varfiles to be used as a virtual normal. This file should contain 1 file location per line, e.g.
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12
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13 /path/to/normal-varfile-1
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14 /path/to/normal-varfile-2
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15 /path/to/normal-varfile-3
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16 /path/to/normal-varfile-4
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17 /path/to/normal-varfile-5
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18 /path/to/normal-varfile-6
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19 /path/to/normal-varfile-7
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20 /path/to/normal-varfile-8
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21 ...
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22
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23 - edit the tool xml file to offer one or more different sets of virtual normals:
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24
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25 [..]
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26 <!-- edit these options to reflect sets of normal you have available. The values must name files within the directories specified in data_table_conf.xml file -->
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27 <param name="VNset" type="select" label="Select Virtual Normal set to use" help="1000Genomes set can only be used for hg19 samples, for hg18 54 genomes will be used.">
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28 <option value="46_diversity.txt" > CG Diversity Panel and trios (54 Genomes) </option>
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29 <option value="433_1000g.txt" > CG 1000G project genomes (433 Genomes) (hg19 only) </option>
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30 <option value="479_diversity_1000g.txt" > Diversity and 1000G (479 genomes) (hg19 only) </option>
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31 <option value="10_tutorial.txt" > Small VN for tutorial (10 Genomes) </option>
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32 </param>
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33 [..]
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34
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35 the values indicate files expected to be at the location configured in the loc file,
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36
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37
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38 So if your .loc file looks like this:
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39
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40
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41 #loc file for virtual normal tool
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42 # <columns>value, dbkey, name, VN_genomes_varfiles_lists_location, VN_genomes_junctionfile_lists_location, reference_crr_cgatools</columns>
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43
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44 hg18 hg18 Virtual Normal hg18 /path/to/VN_genomes_varfiles_lists_hg18/ /path/to/VN_genomes_junctionfiles_lists_hg18/ /path/to/hg18.crr
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45 hg19 hg19 Virtual_Normal hg19 /path/to/VN_genomes_varfiles_lists_hg19/ /path/to/VN_genomes_junctionfiles_lists_hg19/ /path/to/hg19.crr
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46
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47 And your xml file like the example above, then the tool expects the following files to exist:
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48 /path/to/VN_genomes/varfiles_list_hg18/46_diversity.txt
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49 /path/to/VN_genomes/varfiles_list_hg18/433_1000g.txt
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50 ...etc..
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51
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52 and each of these files must contain a 1-per-line list of locations of the varfiles of the normal genomes (or junction files in case of SV analysis).
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53
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54 Varfiles can be in compressed or uncompressed form. For example, Complete Genomics' Diversity panel can be used.
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55 (can be downloaded from ftp://ftp2.completegenomics.com/)
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56
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57
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58
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59 2) restart Galaxy for changes to take effect (alternatively, in the admin panel these setting can be reloaded without the need to restart your galaxy instance)
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60
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61 After this initial setup, additional normals can be added to the lists without having to restart Galaxy.
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