MATCHCLIP

A legacy tool for detecting copy number variation (CNV) breakpoints. The algorithm identified the breakpoint CIGAR strings of reads and their positions. See links for the updated version.

Topic

Biology; Genetics

Details

Operation: Variation detection
Software interface: Command-line user interface
Language: C++
Operating system: Linux
License: GNU General Public License v3

Cost

Version name: -

Maturity:

Credit: NIH grants CA127334, GM097525, EY020483 and EY021451.
Contact: Hongzhe Li hongzhe _at_ upenn.edu
Collection: -

Publications

Wu Y, Tian L, Pirastu M, Stambolian D, Li H "MATCHCLIP: locate precise breakpoints for copy number variation using CIGAR string by matching soft clipped reads." Front Genet. 2013 Aug 16;4:157. https://doi.org/10.3389/fgene.2013.00157
PMID: 23967014
PMCID: PMC3744852

Download and documentation

Source: https://github.com/yhwu/matchclips/
Documentation: https://github.com/yhwu/matchclips/blob/
master/README.md
Home page: https://github.com/yhwu/matchclips/
Links: /tools/cnv/descriptions/matchclips2.html

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MATCHCLIP

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