Structural variant and indel caller for mapped sequencing data
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README.md

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 for a full description of capabilities and limitations.

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

...and the corresponding open-access pre-print.

License

Manta source code is provided under the GPLv3 license. Manta includes several third party packages provided under other open source licenses, please see 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, this distribution can be unpacked, moved to any convenient directory and tested by running a small demo included with the release distribution. Manta can also be installed and run on OS X. Please see the installation instructions for full build and installation details of all supported cases.

Data Analysis and Interpretation

After completing installation, see the Manta user guide 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. This includes details on Manta's developement protocols, special build instructions, recommended workflows for investigating calls, and internal documentation details.