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Mendelian-inheritance-AtTEntive CLique-Enumerating Variant finder MATE-CLEVER

An approach that accurately discovers and genotypes indels longer than 30 bp from contemporary NGS reads with a special focus on family data. For enhanced quality of indel calls in family trios or quartets, MATE-CLEVER integrates statistics that reflect the laws of Mendelian inheritance. MATE-CLEVER's performance rates for indels longer than 30 bp are on a par with those of the GATK for indels shorter than 30 bp, achieving up to 90% precision overall, with >80% of calls correctly typed. In predicting de novo indels longer than 30 bp in family contexts, MATE-CLEVER even raises the standards of the GATK.

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MATE-CLEVER forum

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MATE-CLEVER classification

MATE-CLEVER specifications

Software type:
Package/Module
Restrictions to use:
None
Programming languages:
C++, Python
Computer skills:
Advanced
Maintained:
Yes
Interface:
Command line interface
Operating system:
Unix/Linux
License:
GNU General Public License version 2.0
Stability:
Stable

MATE-CLEVER distribution

versioning

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No versioning.

MATE-CLEVER support

Documentation

Maintainer

  • Tobias Marschall <>

Credits

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Publications

Institution(s)

Centrum Wiskunde & Informatica (CWI), Life Sciences Group, Amsterdam, Netherlands and Department of Computer Science; Brown University, Providence, RI, USA

Link to literature

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