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https://github.com/Illumina/manta

Structural variant and indel caller for mapped sequencing data
https://github.com/Illumina/manta

bioinformatics indels structural-variation structural-variations

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Structural variant and indel caller for mapped sequencing data

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README 

        
Manta Structural Variant Caller

===============================



Manta calls structural variants (SVs) and indels from mapped

paired-end sequencing reads. It is optimized for analysis of germline

variation in small sets of individuals and somatic variation in

tumor/normal sample pairs. Manta discovers, assembles and scores

large-scale SVs, medium-sized indels and large insertions within a

single efficient workflow. The method is designed for rapid analysis

on standard compute hardware: NA12878 at 50x genomic coverage is

analyzed in less than 20 minutes on a 20 core server, and 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 small sets of diploid samples and somatic variants in

matched tumor/normal sample pairs. There is experimental support for

analysis of unmatched tumor samples as well. Manta accepts input read

mappings from BAM or CRAM files and reports all SV and indel inferences

in VCF 4.1 format. See the [user guide][UserGuide] for a full

description of capabilities and limitations.



[UserGuide]:docs/userGuide/README.md



Methods and benchmarking details are described in:



Chen, X. *et al.* (2016) Manta: rapid detection of structural variants and

indels for germline and cancer sequencing applications. *Bioinformatics*,

32, 1220-1222. [doi:10.1093/bioinformatics/btv710][bpaper]



...and the corresponding [open-access pre-print][preprint].



[bpaper]:https://doi.org/10.1093/bioinformatics/btv710

[preprint]:https://doi.org/10.1101/024232



License

-------



Manta source code is provided under the [GPLv3 license](LICENSE.txt).

Manta includes several third party packages provided under other

open source licenses, please see [COPYRIGHT.txt](COPYRIGHT.txt)

for additional details.



Getting Started

---------------



For linux users, it is recommended to start from the most recent

[binary distribution on the Manta releases page][releases], this

distribution can be unpacked, moved to any convenient directory and

tested by [running a small demo](docs/userGuide/installation.md#demo)

included with the release distribution. Manta can also be installed

and run on OS X. Please see the [installation instructions](docs/userGuide/installation.md)

for full build and installation details of all supported cases.



[releases]:https://github.com/Illumina/manta/releases



Data Analysis and Interpretation

--------------------------------



After completing installation, see the [Manta user guide][UserGuide]

for instructions on how to run Manta, interpret results and estimate

hardware requirements/compute cost, in addition to a high-level methods

overview.



Manta Code Development

----------------------



For manta code development and debugging details, see the

[Manta developer guide][DeveloperGuide]. This includes details

on Manta's developement protocols, special build instructions,

recommended workflows for investigating

calls, and internal documentation details.



[DeveloperGuide]:docs/developerGuide/README.md