Mercurial > repos > saskia-hiltemann > virtual_normal_analysis

comparison README.txt @ 2:885ba15c2564 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author saskia-hiltemann
date Mon, 03 Aug 2015 05:45:16 -0400
parents 1209f18a5a83
children ac09a5aaed0b
comparison
equal deleted inserted replaced
1:1c6710924e80 2:885ba15c2564
5 1) edit virtual_normal_correction.loc file 5 1) edit virtual_normal_correction.loc file
6 6
7 - change "/path/to/hg18.crr" to the location of the Complete Genomics reference crr file on your system 7 - change "/path/to/hg18.crr" to the location of the Complete Genomics reference crr file on your system
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_hg18.txt" to the location of the file containing 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
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 Varfiles can be in compressed or uncompressed form. For example, Complete Genomics' Diversity panel can be used. 23 - edit the tool xml file to offer sets of virtual normals
24
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 -->
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>
29 <option value="433_1000g.txt" > CG 1000G project genomes (433 Genomes) (hg19 only) </option>
30 <option value="479_diversity_1000g.txt" > Diversity and 1000G (479 genomes) (hg19 only) </option>
31 <option value="10_tutorial.txt" > Small VN for tutorial (10 Genomes) </option>
32 </param>
33 [..]
34
35 the values indicate files expected to be at the location configured in the loc file,
36
37
38 So if your .loc file looks like this:
39
40
41 #loc file for annovar tool
42
43 # <columns>value, dbkey, name, VN_genomes_varfiles_list, VN_genomes_junctionfile_list, reference_crr_cgatools</columns>
44
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
48 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
50 /path/to/VN_genomes/varfiles_list_hg18/433_1000g.txt
51 etc
52 and containing a 1-per-line list of locations of the varfiles of the normal genomes.
53
54
55
56
57 Varfiles can be in compressed or uncompressed form. For example, Complete Genomics' Diversity panel can be used.
24 (can be downloaded from ftp://ftp2.completegenomics.com/) 58 (can be downloaded from ftp://ftp2.completegenomics.com/)
25 59
26 - change "/path/to/VN_genomes_junctionfiles_hg18.txt" to the location of the file containing the locations of all the Complete Genomics 60 - change "/path/to/VN_genomes_junctionfiles_lists_hg18" to the location of the file containing the locations of all the Complete Genomics
27 junctionfiles to be used as a virtual normal. This file should contain 1 file location per line. For example, Complete Genomics' 61 junctionfiles to be used as a virtual normal. This file should contain 1 file location per line. For example, Complete Genomics'
28 Diversity panel can be used. (can be downloaded from ftp://ftp2.completegenomics.com/) 62 Diversity panel can be used. (can be downloaded from ftp://ftp2.completegenomics.com/)
29 63
30 2) restart Galaxy for changes to take effect 64 2) restart Galaxy for changes to take effect
31 65