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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_hg18.txt" to the location of the file containing 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 Varfiles can be in compressed or uncompressed form. For example, Complete Genomics' Diversity panel can be used.
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24 (can be downloaded from ftp://ftp2.completegenomics.com/)
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25
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26 - change "/path/to/VN_genomes_junctionfiles_hg18.txt" to the location of the file containing the locations of all the Complete Genomics
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27 junctionfiles to be used as a virtual normal. This file should contain 1 file location per line. For example, Complete Genomics'
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28 Diversity panel can be used. (can be downloaded from ftp://ftp2.completegenomics.com/)
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29
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30 2) restart Galaxy for changes to take effect
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31
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32 After this initial setup, additional normals can be added to the lists without having to restart Galaxy.
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