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Calls structural variants (SVs) and indels from mapped paired-end sequencing reads. Manta is optimized for analysis of individuals and tumor/normal sample pairs, calling SVs, medium-sized indels and large insertions within a single workflow. The method is designed for rapid analysis on standard computer hardware: NA12878 at 50x genomic coverage is analyzed in less than 20 minutes on a 20 core server, most WGS tumor-normal analyses can be completed within 2 hours. Manta combines paired and split-read evidence during SV discovery and scoring to improve accuracy, but does not require split-reads or successful breakpoint assemblies to report a variant in cases where there is strong evidence otherwise. It provides scoring models for germline variants in individual diploid samples and somatic variants in matched tumor-normal sample pairs.

Software type:
Package
Interface:
Command line interface
Restrictions to use:
None
Input data:
Sequence data
Input format:
BAM
Output data:
Variant calls
Output format:
VCF
Biological technology:
Illumina
Operating system:
Unix/Linux, Mac OS
Programming languages:
C++, Python
License:
GNU General Public License version 2.0
Computer skills:
Advanced
Version:
Manta version 0.26.4
Stability:
Stable
Requirements:
python 2.4+, gcc 4.7+ or clang 3.1+ (or Visual Studio 2013+), libz (including headers)
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Links

Maintainer

  • Christopher Saunders <csaunders at illumina.com>

Institution(s)

Illumina, Inc, 5200 Illumina Way, San Diego, CA 92122, USA; Illumina Cambridge Ltd., Chesterford Research Park, Little Chesterford, Essex CB10 1XL, UK

  • (Chen et al., 2015) Manta: rapid detection of structural variants and indels for germline and cancer sequencing applications. Bioinformatics.
    PMID: 26647377

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