AB Inversion Tool

Description

• In this tool an inversion is defined by its two breakpoints. The numbers of mate pairs supporting occurrence of the starting and ending inversion breakpoints are counted for each base pair. The genomic ranges corresponding to local peaks of these counts, if above a score threshold, are called as candidate breakpoint ranges. To define an inversion, its starting and ending breakpoints are paired up only if they are the reciprocal nearest neighbor of each other in the correct order. The score for such the inversion is the harmonic mean of its two breakpoints. Finally, each breakpoint range is scanned for coverage of normal (AAA) mate pairs to identify a sub-range with the lowest normal mate pair coverage as the most probable location of a breakpoint and to differentiate homozygous inversions from heterozygous ones. The supporting evidence of all inversions can be visually inspected using SOLID Alignment Browser (SAB).

Licensing

• This software is being licensed to you under the OSI compliant GNU Public License (GPL). Please read the license in its entirety and ensure that you understand the licensing conditions for use. Your use of this software indicates your acceptance of this licensing agreement. Click on this link to read the licensing agreement.

Support

• This tool is being released as "unsupported software" by Applied Biosystems

Packages

Pre-Bioscope™ Tool

• The current version of the tool can be downloaded here.
• Documentation and Release notes for this software can be found here.
• A sample dataset can be downloaded here.

Source Distribution (please note that this is a source ONLY distribution of a Bioscope algorithm and available through SVN checkout)

• Please contact website support to recieve access information
• The current version of the source can be downloaded here.
• Documentation and Release notes for this software can be found here.
• A sample dataset can be downloaded here