Mercurial > repos > saskia-hiltemann > virtual_normal_analysis
changeset 3:ac09a5aaed0b draft
Uploaded
| author | saskia-hiltemann |
|---|---|
| date | Mon, 03 Aug 2015 06:00:51 -0400 |
| parents | 885ba15c2564 |
| children | 58815aed4ec3 |
| files | README.txt VN_genomes_locations.txt tool-data/virtual_normal_correction.loc.sample |
| diffstat | 3 files changed, 38 insertions(+), 37 deletions(-) [+] |
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--- a/README.txt Mon Aug 03 05:45:16 2015 -0400 +++ b/README.txt Mon Aug 03 06:00:51 2015 -0400 @@ -10,17 +10,17 @@ - change "/path/to/VN_genomes_varfiles_lists_hg18" to the location of the directory containing files with the locations of all the Complete Genomics varfiles to be used as a virtual normal. This file should contain 1 file location per line, e.g. - /path/to/normal-varfile-1 - /path/to/normal-varfile-2 - /path/to/normal-varfile-3 - /path/to/normal-varfile-4 - /path/to/normal-varfile-5 - /path/to/normal-varfile-6 - /path/to/normal-varfile-7 - /path/to/normal-varfile-8 + /path/to/normal-varfile-1 + /path/to/normal-varfile-2 + /path/to/normal-varfile-3 + /path/to/normal-varfile-4 + /path/to/normal-varfile-5 + /path/to/normal-varfile-6 + /path/to/normal-varfile-7 + /path/to/normal-varfile-8 ... - - edit the tool xml file to offer sets of virtual normals + - edit the tool xml file to offer one or more different sets of virtual normals: [..] <!-- 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 --> @@ -38,29 +38,24 @@ So if your .loc file looks like this: - #loc file for annovar tool + #loc file for virtual normal tool + # <columns>value, dbkey, name, VN_genomes_varfiles_lists_location, VN_genomes_junctionfile_lists_location, reference_crr_cgatools</columns> - # <columns>value, dbkey, name, VN_genomes_varfiles_list, VN_genomes_junctionfile_list, reference_crr_cgatools</columns> - - hg18 hg18 Virtual Normal hg18 /path/to/VN_genomes_varfiles_lists_hg18 /path/to/VN_genomes_junctionfiles_lists_hg18 /path/to/hg18.crr - hg19 hg19 Virtual_Normal hg19 /path/to/VN_genomes_varfiles_lists_hg19 /path/to/VN_genomes_junctionfiles_lists_hg19 /path/to/hg19.crr + hg18 hg18 Virtual Normal hg18 /path/to/VN_genomes_varfiles_lists_hg18/ /path/to/VN_genomes_junctionfiles_lists_hg18/ /path/to/hg18.crr + hg19 hg19 Virtual_Normal hg19 /path/to/VN_genomes_varfiles_lists_hg19/ /path/to/VN_genomes_junctionfiles_lists_hg19/ /path/to/hg19.crr And your xml file like the example above, then the tool expects the following files to exist: /path/to/VN_genomes/varfiles_list_hg18/46_diversity.txt /path/to/VN_genomes/varfiles_list_hg18/433_1000g.txt - etc - and containing a 1-per-line list of locations of the varfiles of the normal genomes. + ...etc.. - - + 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). Varfiles can be in compressed or uncompressed form. For example, Complete Genomics' Diversity panel can be used. (can be downloaded from ftp://ftp2.completegenomics.com/) - - - change "/path/to/VN_genomes_junctionfiles_lists_hg18" to the location of the file containing the locations of all the Complete Genomics - junctionfiles to be used as a virtual normal. This file should contain 1 file location per line. For example, Complete Genomics' - Diversity panel can be used. (can be downloaded from ftp://ftp2.completegenomics.com/) + + - 2) restart Galaxy for changes to take effect + 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) After this initial setup, additional normals can be added to the lists without having to restart Galaxy.
--- a/VN_genomes_locations.txt Mon Aug 03 05:45:16 2015 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,8 +0,0 @@ -/path/to/normal-varfile-1 -/path/to/normal-varfile-2 -/path/to/normal-varfile-3 -/path/to/normal-varfile-4 -/path/to/normal-varfile-5 -/path/to/normal-varfile-6 -/path/to/normal-varfile-7 -/path/to/normal-varfile-8
--- a/tool-data/virtual_normal_correction.loc.sample Mon Aug 03 05:45:16 2015 -0400 +++ b/tool-data/virtual_normal_correction.loc.sample Mon Aug 03 06:00:51 2015 -0400 @@ -1,6 +1,20 @@ -#loc file for annovar tool - -# <columns>value, dbkey, name, VN_genomes_varfiles_list, VN_genomes_junctionfile_list, reference_crr_cgatools</columns> - -#hg18 hg18 Virtual Normal hg18 /path/to/VN_genomes_varfiles_lists_hg18 /path/to/VN_genomes_junctionfiles_lists_hg18 /path/to/hg18.crr -#hg19 hg19 Virtual_Normal hg19 /path/to/VN_genomes_varfiles_lists_hg19 /path/to/VN_genomes_junctionfiles_lists_hg19 /path/to/hg19.crr +# loc file for virtual normal tool +# +# <columns>value, dbkey, name, VN_genomes_varfiles_lists_location, VN_genomes_junctionfile_lists_location, reference_crr_cgatools</columns> +# +# +# The column "VN_genomes_varfiles_lists_location" indicates the directory Galaxy will expect files containing the locations of different sets of normal varfiles to be. +# If the tool xml file contains the following: +# +# <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."> +# <option value="46_diversity.txt" > CG Diversity Panel and trios (54 Genomes) </option> +# <option value="433_1000g.txt" > CG 1000G project genomes (433 Genomes) (hg19 only) </option> +# </param> +# +# then the files 46_diversity.txt and 433_1000g.txt are expected to be at the locations configured below. +# These txt files should contain the locations of the normals on the system, in a 1-per-line format (list of varfiles for small variant correction, list of junction files for SV analysis) +# +# <columns>value, dbkey, name, VN_genomes_varfiles_lists_location, VN_genomes_junctionfile_lists_location, reference_crr_cgatools</columns> +# +#hg18 hg18 Virtual Normal hg18 /path/to/VN_genomes_varfiles_lists_hg18/ /path/to/VN_genomes_junctionfiles_lists_hg18/ /path/to/hg18.crr +#hg19 hg19 Virtual_Normal hg19 /path/to/VN_genomes_varfiles_lists_hg19/ /path/to/VN_genomes_junctionfiles_lists_hg19/ /path/to/hg19.crr