MATE-CLEVER statistics

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MATE-CLEVER specifications


Unique identifier OMICS_00309
Alternative names Mendelian-inheritance-AtTEntive CLique-Enumerating Variant finder, The CLEVER Toolkit, CTK
Software type Toolkit/Suite
Interface Command line interface
Restrictions to use None
Biological technology Illumina
Operating system Unix/Linux
Programming languages C++, Python
License GNU General Public License version 3.0
Computer skills Advanced
Version 2.3
Stability Stable
boost, cmake, zlib
Maintained Yes




No version available



  • person_outline Tobias Marschall
  • person_outline Alexander Schönhuth
  • person_outline CLEVER Team

Publications for Mendelian-inheritance-AtTEntive CLique-Enumerating Variant finder

MATE-CLEVER citations


A high quality human reference panel reveals the complexity and distribution of genomic structural variants

Nat Commun
PMCID: 5059695
PMID: 27708267
DOI: 10.1038/ncomms12989
call_split See protocol

[…] To genotype SVs, we used GATK's HaplotypeCaller for complex indels, MATE-CLEVER for deletions, Mobster for MEIs and Delly for inversions, duplications, and translocations. Details on how each tool was run are collected in . For phasing, we used the haplotype scaffolds […]


Deletion of Indian hedgehog gene causes dominant semi lethal Creeper trait in chicken

Sci Rep
PMCID: 4954956
PMID: 27439785
DOI: 10.1038/srep30172

[…] 5-read mapping depth and mapping quality of 20. As indels ranged from 1 to 1000 bp, we used three different algorithms to search for indels. The GATK software is suitable for detecting small indels. Mate-Clever is more suitable to probe the medium-size indels from the resequencing data than GATK and was thus used to find the medium-size indels. We used Pindel (version 0.2.4t) to detect large stru […]


Detection of Genomic Structural Variants from Next Generation Sequencing Data

Front Bioeng Biotechnol
PMCID: 4479793
PMID: 26161383
DOI: 10.3389/fbioe.2015.00092

[…] ral polymorphisms.Packages implementing RP and (local) AS have been also reported [NovelSeq (Hajirasouliha et al., ), HYDRA (Quinlan et al., )] as well as tools exploiting SR and RC/RP such as SVseq, MATE-CLEVER, and PRISM (Zhang and Wu, ; Jiang et al., ; Marschall et al., ). PRISM was tested on simulated data and compared with Pindel, SVseq, Splitread, and CREST. Notably, DELLY is suitable for de […]


Using familial information for variant filtering in high throughput sequencing studies

Hum Genet
PMCID: 4185103
PMID: 25129038
DOI: 10.1007/s00439-014-1479-4

[…] om HTS data by making use of variant callers that incorporate familial information. FamSeq (Peng et al. ) and PolyMutt (Li et al. ) improve variant calling by making use of familial information while MATE-CLEVER (Marschall et al. ) performs family aware indel detection and calling. Once HapMap SNP genotypes are called, Mendelian error checking can be performed via LINKDATAGEN (nuclear family Mende […]


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


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