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Repository count_roi_variants
Name: count_roi_variants
Owner: peterjc
Synopsis: Count sequence variants in region of interest in BAM file
This tool runs the command ``samtools view`` (taking advantage of an
indexed BAM file) to access only those reads mapped to the region of
interest (ROI), and then counts the different sequence variants found.
Content homepage: https://github.com/peterjc/pico_galaxy/tree/master/tools/count_roi_variants
Development repository: https://github.com/peterjc/pico_galaxy/tree/master/tools/count_roi_variants
Link to this repository: https://toolshed.g2.bx.psu.edu/view/peterjc/count_roi_variants/167765a633c0
Clone this repository: hg clone https://toolshed.g2.bx.psu.edu/repos/peterjc/count_roi_variants
Type: unrestricted
Revision: 2:167765a633c0
This revision can be installed: True
Times cloned / installed: 207
Dependencies of this repository

Repository dependencies - installation of these additional repositories is required
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)

Tool dependencies - repository tools require handling of these dependencies
Name Version Type
samtools 1.2 package

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
using samtools view 0.0.6 16.01

Categories
Assembly - Tools for working with assemblies
SAM - Tools for manipulating alignments in the SAM format