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Repository extractsplitreads_bwamem
Name: extractsplitreads_bwamem
Owner: hepcat72
Synopsis: A wrapper for version 0.1.0 of the extractSplitReads_BwaMem script that comes with lumpy-sv version 0.2.14a.
Get split-read alignments from bwa-mem in lumpy compatible format. Ignores reads marked as duplicates. Works on read or position sorted SAM input. Tested on bwa mem v0.7.5a-r405.
Content homepage: https://github.com/arq5x/lumpy-sv
Link to this repository: https://toolshed.g2.bx.psu.edu/view/hepcat72/extractsplitreads_bwamem/a20ac5d90c16
Clone this repository: hg clone https://toolshed.g2.bx.psu.edu/repos/hepcat72/extractsplitreads_bwamem
Type: unrestricted
Revision: 1:a20ac5d90c16
This revision can be installed: True
Times cloned / installed: 287

Contents of this repository

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Name Description Version Minimum Galaxy Version
from bwaMEM (part of lumpy-sv) 0.1.0 16.01

Categories
SAM - Tools for manipulating alignments in the SAM format
Variant Analysis - Tools for single nucleotide polymorphism data such as WGA