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Manta specifications


Unique identifier OMICS_09180
Name Manta
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input data A sequence data file.
Input format BAM
Output data Some variant calls.
Output format VCF
Biological technology Illumina
Operating system Unix/Linux, Mac OS
Programming languages C++, Python
License GNU General Public License version 3.0
Computer skills Advanced
Version 1.4.0
Stability Stable
GCC or clang, libz
Maintained Yes




No version available



  • person_outline Christopher Saunders

Publication for Manta

Manta citations


Molecular, Pathological, Radiological, and Immune Profiling of Non brainstem Pediatric High Grade Glioma from the HERBY Phase II Randomized Trial

Cancer Cell
PMCID: 5956280
PMID: 29763623
DOI: 10.1016/j.ccell.2018.04.004
call_split See protocol

[…] ries (). NGS fusion panel alignment was performed against the human reference sequence GRCh37/Hg19. Quality control (QC), variant annotation, deduplication and metrics were generated for each sample. Manta ( and Breakdancer ( were used for the detection of structural variants. […]


Rapid whole genome sequencing decreases infant morbidity and cost of hospitalization

PMCID: 5884823
PMID: 29644095
DOI: 10.1038/s41525-018-0049-4
call_split See protocol

[…] , table ) and mapped to genetic diagnoses., Trio blood samples were obtained where possible. rWGS was performed to ~45-fold coverage as previously described., Structural variants were identified with Manta and CNVnator, a combination that provided the highest sensitivity and precision on 21 samples with known structural variants., Structural variants were filtered to retain those affecting coding […]


Chromothripsis and ring chromosome 22: a paradigm of genomic complexity in the Phelan McDermid syndrome (22q13 deletion syndrome)

J Med Genet
PMCID: 5869459
PMID: 29378768
DOI: 10.1136/jmedgenet-2017-105125

[…] erage of 1000 bp windows sliding over the whole chromosome length, in order to identify large deletions and duplications in each chromosome. Structural variants were called using Lumpy (V.0.2.12) and Manta (V.0.29.6). Then these structural variants were visualised and manually checked in Integrative Genomics Viewer (IGV) genome browser (V.2.3.72) in order to reconstruct chromosomes showing chromot […]


Mutational signatures reveal the dynamic interplay of risk factors and cellular processes during liver tumorigenesis

Nat Commun
PMCID: 5670220
PMID: 29101368
DOI: 10.1038/s41467-017-01358-x

[…] We used MANTA software to identify somatic structural variations (Supplementary Data ) and viral insertions (Supplementary Table ) from the tumor and non-tumor bam files. To keep only the most reliable events […]


Profiling of Short Tandem Repeat Disease Alleles in 12,632 Human Whole Genomes

Am J Hum Genet
PMCID: 5673627
PMID: 29100084
DOI: 10.1016/j.ajhg.2017.09.013
call_split See protocol

[…] ublicly available (see ).After running EAGLE, we mapped the simulated reads onto the human reference genome hg38 by using the BWA aligner and then ran TREDPARSE and popular variant calling softwares (Manta, Isaac, GATK, lobSTR, and TREDPARSE) and comparing the inferred lengths with the true ones. For the HD locus, the pathological threshold (full-penetrance allele) is established at 40 CAGs, so th […]


Assessment of the incorporation of CNV surveillance into gene panel next generation sequencing testing for inherited retinal diseases

J Med Genet
PMCID: 5800348
PMID: 29074561
DOI: 10.1136/jmedgenet-2017-104791
call_split See protocol

[…] cations of IRD. Six hundred and five samples were generated using Illumina sequencing chemistry as part of the National Institute for Health Research (NIHR) BioResource Rare Diseases project, and the Manta and Canvas software algorithms were used to detect CNVs. Seventy-seven samples were generated using Complete Genomics sequencing chemistry, with CNVs identified using the Complete Genomics V.2.5 […]


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Manta institution(s)
Illumina, Inc, San Diego, CA, USA; Illumina Cambridge Ltd, Little Chesterford, UK

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