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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.

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

Maintainer

  • Tobias Marschall <marschal at mpi-inf.mpg.de>

Institution(s)

Centrum Wiskunde & Informatica (CWI), Life Sciences Group, Science Park 123, Amsterdam 1098 XG, The Netherlands and Department of Computer Science; Brown University, Providence, Rhode Island 02906, USA

  • (Marschall et al., 2013) MATE-CLEVER: Mendelian-inheritance-aware discovery and genotyping of midsize and long indels. Bioinformatics.
    PMID: 24072733

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