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Repository ngsap_vc
Name: ngsap_vc
Owner: scisjnu123
Synopsis: VARIANT CALLING TOOLS AND WORKFLOW
Contains variant calling tools and workflows.
Link to this repository: https://toolshed.g2.bx.psu.edu/view/scisjnu123/ngsap_vc/0d10255b5434
Clone this repository: hg clone https://toolshed.g2.bx.psu.edu/repos/scisjnu123/ngsap_vc
Type: unrestricted
Revision: 3:0d10255b5434
This revision can be installed: True
Times cloned / installed: 228
Dependencies of this repository

Repository dependencies - A suite of Galaxy tools designed to work with version 1.2 of the SAMtools package.
Repository package_samtools_0_1_19 revision 95d2c4aefb5f owned by devteam
Repository package_samtools_1_2 revision f6ae3ba3f3c1 owned by iuc
Repository package_ncurses_5_9 revision 335ebf512407 owned by iuc (prior install required)
Repository package_zlib_1_2_8 revision 411985b46ae8 owned by iuc (prior install required)
Repository package_samtools_1_2 revision f6ae3ba3f3c1 owned by iuc
Repository package_samtools_1_2 revision f6ae3ba3f3c1 owned by iuc
Repository package_samtools_1_2 revision f6ae3ba3f3c1 owned by iuc
Repository package_samtools_1_2 revision f6ae3ba3f3c1 owned by iuc
Repository package_samtools_1_2 revision f6ae3ba3f3c1 owned by iuc
Repository package_samtools_1_2 revision f6ae3ba3f3c1 owned by iuc
Repository package_samtools_1_2 revision f6ae3ba3f3c1 owned by iuc
Repository package_samtools_1_2 revision f6ae3ba3f3c1 owned by iuc
Repository package_samtools_1_2 revision f6ae3ba3f3c1 owned by iuc
Repository package_samtools_1_2 revision f6ae3ba3f3c1 owned by iuc
Repository package_samtools_1_2 revision f6ae3ba3f3c1 owned by iuc
Repository package_samtools_1_2 revision f6ae3ba3f3c1 owned by iuc
Repository package_r_3_1_2 revision 4d2fd1413b56 owned by iuc (prior install required)
Repository package_readline_6_2 revision 5313ca2fbce6 owned by iuc (prior install required)
Repository package_libpng_1_6_7 revision 3de32cd300a9 owned by devteam (prior install required)
Repository package_cairo_1_12_14 revision cd2ed5717e38 owned by devteam (prior install required)
Repository package_pixman_0_32_4 revision 93cd8e03820c owned by devteam (prior install required)
Repository package_freetype_2_5_2 revision a65217367e4a owned by devteam (prior install required)
Repository package_ncurses_5_9 revision 335ebf512407 owned by iuc (prior install required)
Repository package_fontconfig_2_11_1 revision d88d844df0cb owned by iuc (prior install required)
Repository package_ncurses_5_9 revision 335ebf512407 owned by iuc (prior install required)
Repository package_pixman_0_32_4 revision 93cd8e03820c owned by devteam (prior install required)
Repository package_libpng_1_6_7 revision 3de32cd300a9 owned by devteam (prior install required)
Repository package_freetype_2_5_2 revision a65217367e4a owned by devteam (prior install required)
Repository package_fontconfig_2_11_1 revision d88d844df0cb owned by iuc (prior install required)
Repository package_libpng_1_6_7 revision 3de32cd300a9 owned by devteam (prior install required)
Repository package_libpng_1_6_7 revision 3de32cd300a9 owned by devteam (prior install required)
Repository package_freetype_2_5_2 revision 1e86d1cf79a4 owned by iuc (prior install required)
Repository package_libxml2_2_9_1 revision 45b16a3ab504 owned by iuc (prior install required)
Repository package_zlib_1_2_8 revision 411985b46ae8 owned by iuc (prior install required)
Repository package_libpng_1_6_7 revision 588666932a32 owned by iuc (prior install required)
Repository package_zlib_1_2_8 revision 411985b46ae8 owned by iuc (prior install required)

Tool dependencies - repository tools require handling of these dependencies
Name Version Type
package_r_for_gatk_3_4_0 3.1.2.1 package
GATK_PATH set_environment
GATK_SITE_OPTIONS set_environment

Contents of this repository

Valid tools - click the name to preview the tool and use the pop-up menu to inspect all metadata
Name Description Version Minimum Galaxy Version
tool collection Version 3.4-0 3.4-0.d9 16.01
somatic mutation caller for cancer genomics 2.3.5 16.01
mutation caller for targeted, exome, and whole-genome resequencing 2.3.5 16.01
BAM, chromosome info or sv files 1.0.0 16.01
structural variants between two samples 1.0.0 16.01
to get abnormal pairs 1.0.0 16.01
plots 1.1.0 16.01
and identify structural variants 1.0.0 16.01

Categories
Variant Analysis - Tools for single nucleotide polymorphism data such as WGA