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comparison README.txt @ 3:ac09a5aaed0b draft

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author saskia-hiltemann
date Mon, 03 Aug 2015 06:00:51 -0400
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2:885ba15c2564 3:ac09a5aaed0b
8 (can be downloaded from ftp://ftp.completegenomics.com/ReferenceFiles/ ) 8 (can be downloaded from ftp://ftp.completegenomics.com/ReferenceFiles/ )
9 9
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 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
11 varfiles to be used as a virtual normal. This file should contain 1 file location per line, e.g. 11 varfiles to be used as a virtual normal. This file should contain 1 file location per line, e.g.
12 12
13 /path/to/normal-varfile-1 13 /path/to/normal-varfile-1
14 /path/to/normal-varfile-2 14 /path/to/normal-varfile-2
15 /path/to/normal-varfile-3 15 /path/to/normal-varfile-3
16 /path/to/normal-varfile-4 16 /path/to/normal-varfile-4
17 /path/to/normal-varfile-5 17 /path/to/normal-varfile-5
18 /path/to/normal-varfile-6 18 /path/to/normal-varfile-6
19 /path/to/normal-varfile-7 19 /path/to/normal-varfile-7
20 /path/to/normal-varfile-8 20 /path/to/normal-varfile-8
21 ... 21 ...
22 22
23 - edit the tool xml file to offer sets of virtual normals 23 - edit the tool xml file to offer one or more different sets of virtual normals:
24 24
25 [..] 25 [..]
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 --> 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 -->
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."> 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.">
28 <option value="46_diversity.txt" > CG Diversity Panel and trios (54 Genomes) </option> 28 <option value="46_diversity.txt" > CG Diversity Panel and trios (54 Genomes) </option>
36 36
37 37
38 So if your .loc file looks like this: 38 So if your .loc file looks like this:
39 39
40 40
41 #loc file for annovar tool 41 #loc file for virtual normal tool
42 # <columns>value, dbkey, name, VN_genomes_varfiles_lists_location, VN_genomes_junctionfile_lists_location, reference_crr_cgatools</columns>
42 43
43 # <columns>value, dbkey, name, VN_genomes_varfiles_list, VN_genomes_junctionfile_list, reference_crr_cgatools</columns> 44 hg18 hg18 Virtual Normal hg18 /path/to/VN_genomes_varfiles_lists_hg18/ /path/to/VN_genomes_junctionfiles_lists_hg18/ /path/to/hg18.crr
44 45 hg19 hg19 Virtual_Normal hg19 /path/to/VN_genomes_varfiles_lists_hg19/ /path/to/VN_genomes_junctionfiles_lists_hg19/ /path/to/hg19.crr
45 hg18 hg18 Virtual Normal hg18 /path/to/VN_genomes_varfiles_lists_hg18 /path/to/VN_genomes_junctionfiles_lists_hg18 /path/to/hg18.crr
46 hg19 hg19 Virtual_Normal hg19 /path/to/VN_genomes_varfiles_lists_hg19 /path/to/VN_genomes_junctionfiles_lists_hg19 /path/to/hg19.crr
47 46
48 And your xml file like the example above, then the tool expects the following files to exist: 47 And your xml file like the example above, then the tool expects the following files to exist:
49 /path/to/VN_genomes/varfiles_list_hg18/46_diversity.txt 48 /path/to/VN_genomes/varfiles_list_hg18/46_diversity.txt
50 /path/to/VN_genomes/varfiles_list_hg18/433_1000g.txt 49 /path/to/VN_genomes/varfiles_list_hg18/433_1000g.txt
51 etc 50 ...etc..
52 and containing a 1-per-line list of locations of the varfiles of the normal genomes.
53 51
54 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).
55
56 53
57 Varfiles can be in compressed or uncompressed form. For example, Complete Genomics' Diversity panel can be used. 54 Varfiles can be in compressed or uncompressed form. For example, Complete Genomics' Diversity panel can be used.
58 (can be downloaded from ftp://ftp2.completegenomics.com/) 55 (can be downloaded from ftp://ftp2.completegenomics.com/)
59 56
60 - change "/path/to/VN_genomes_junctionfiles_lists_hg18" to the location of the file containing the locations of all the Complete Genomics 57
61 junctionfiles to be used as a virtual normal. This file should contain 1 file location per line. For example, Complete Genomics'
62 Diversity panel can be used. (can be downloaded from ftp://ftp2.completegenomics.com/)
63 58
64 2) restart Galaxy for changes to take effect 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)
65 60
66 After this initial setup, additional normals can be added to the lists without having to restart Galaxy. 61 After this initial setup, additional normals can be added to the lists without having to restart Galaxy.