# manta

**Repository Path**: Magic-Frog/manta

## Basic Information

- **Project Name**: manta
- **Description**: 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 (see details below). Manta accepts input read mappings from BAM or CRAM files and reports all SV and indel inferences in VCF 4.1 format.
- **Primary Language**: Unknown
- **License**: Not specified
- **Default Branch**: master
- **Homepage**: None
- **GVP Project**: No

## Statistics

- **Stars**: 0
- **Forks**: 1
- **Created**: 2022-09-07
- **Last Updated**: 2022-09-07

## Categories & Tags

**Categories**: Uncategorized

**Tags**: None

## README

# manta

#### Description
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 (see details below). Manta accepts input read mappings from BAM or CRAM files and reports all SV and indel inferences in VCF 4.1 format.

#### Software Architecture
Software architecture description

#### Installation

1.  xxxx
2.  xxxx
3.  xxxx

#### Instructions

1.  xxxx
2.  xxxx
3.  xxxx

#### Contribution

1.  Fork the repository
2.  Create Feat_xxx branch
3.  Commit your code
4.  Create Pull Request


#### Gitee Feature

1.  You can use Readme\_XXX.md to support different languages, such as Readme\_en.md, Readme\_zh.md
2.  Gitee blog [blog.gitee.com](https://blog.gitee.com)
3.  Explore open source project [https://gitee.com/explore](https://gitee.com/explore)
4.  The most valuable open source project [GVP](https://gitee.com/gvp)
5.  The manual of Gitee [https://gitee.com/help](https://gitee.com/help)
6.  The most popular members  [https://gitee.com/gitee-stars/](https://gitee.com/gitee-stars/)