Manta protocols

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Manta specifications

Information


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
Requirements
GCC or clang, libz
Maintained Yes

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Maintainer


  • person_outline Christopher Saunders <>

Publication for Manta

Manta in pipelines

 (2)
2017
PMCID: 5535982
PMID: 28696354
DOI: 10.3390/ijms18071492

[…] reads were aligned to the human reference genome (hg19) with the star aligner (v2.5.0a) []. gene fusions were detected in the aligned bam files using the manta software []., the genbank accession number for tmem154-rasgrf1 mrna is mf175878. rna-seq fastq files were submitted to the sequence read archive (sra) with the genbank accession number […]

2017
PMCID: 5800348
PMID: 29074561
DOI: 10.1136/jmedgenet-2017-104791

[…] 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 […]


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Manta in publications

 (13)
PMCID: 5897357
PMID: 29650961
DOI: 10.1038/s41467-018-03672-4

[…] collapsed considering only the protein-coding region in the canonical transcript of the protein-coding genes in the genome assembly grch37., copy number variation was identified using canvas and manta. deletions called by both manta and canvas with a reciprocal overlap of ≥20% were retained. of these, deletions were excluded if both failed standard illumina quality metrics or overlapped […]

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

[…] sample were selected. for indels, we selected mutations with a mutect2 filter flag among “pass”, “clustered_events” or “str_contraction” supported by ≥ 20% reads in the tumor sample., 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 […]

PMCID: 5673627
PMID: 29100084
DOI: 10.1016/j.ajhg.2017.09.013

[…] 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, […]

PMCID: 5559527
PMID: 28814763
DOI: 10.1038/s41467-017-00296-y

[…] threshold for these mutations was ~1.5% (range: 0.4–4%) vaf, corresponding to a ccf of 3% (0.8–8%) for a diploid site and a tumor purity of 100%., ig and myc translocations were called using manta v0.20.2 with a variant quality score threshold of 30. translocation calls were manually inspected in igv. snvs, indels and translocations we annotated using annovar and snpeff v4.2., […]

PMCID: 5460900
PMID: 28531216
DOI: 10.1371/journal.pgen.1006808

[…] annotated using the variant effect predictor (vep release 75) tool []. as described in secrier et al. [], for structural variant calling the reads were mapped to the grch37 reference genome, and manta [] was used to identify putative breakpoint junctions using discordant read pairs and split reads. breakpoints and potential run-through events were annotated using the ensembl grch37, version […]


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

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