1. Directory
  2. Genomics
  3. Genome annotation
  4. Repetitive DNA
Join community Sign in
By using OMICtools you acknowledge that you have read and accepted the terms of the end user license agreement.

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:
Command line interface
Restrictions to use:
Operating system:
Programming languages:
C++, Python
GNU General Public License version 2.0
Computer skills:
View all reviews

0 user review

No review has been posted.

View all issues

0 issue

No open issue.



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


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

58 related tools