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Repository samtools_rmdup
Name: samtools_rmdup
Owner: devteam
Synopsis: Remove PCR duplicates
This tool uses the SAMtools toolkit to remove potential PCR duplicates:
if multiple read pairs have identical external coordinates, only retain the pair
with highest mapping quality. In the paired-end mode, this command ONLY works with
FR orientation and requires ISIZE is correctly set. It does not work for unpaired
reads (e.g. two ends mapped to different chromosomes or orphan reads).
Content homepage: http://www.htslib.org/
Development repository: https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_rmdup
Link to this repository revision: https://toolshed.g2.bx.psu.edu/view/devteam/samtools_rmdup/3735f950b2f5
Clone this repository: hg clone https://toolshed.g2.bx.psu.edu/repos/devteam/samtools_rmdup
Type: unrestricted
Revision: 2:3735f950b2f5
This revision can be installed: True
Times cloned / installed: 9528
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
remove PCR duplicates 2.0 any

Categories
SAM - Tools for manipulating alignments in the SAM format