https://github.com/seqan/vaquita

Identification of structural variations
https://github.com/seqan/vaquita

Last synced: 8 months ago
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Identification of structural variations

• Host: GitHub
• URL: https://github.com/seqan/vaquita
• Owner: seqan
• License: other
• Created: 2017-02-14T16:58:46.000Z (over 9 years ago)
• Default Branch: master
• Last Pushed: 2022-07-22T11:23:16.000Z (almost 4 years ago)
• Last Synced: 2025-03-23T23:27:03.240Z (over 1 year ago)
• Language: C++
• Size: 2.54 MB
• Stars: 12
• Watchers: 2
• Forks: 4
• Open Issues: 11
• Metadata Files:
  • Readme: README.md
  • Changelog: CHANGELOG.txt
  • License: LICENSE.txt

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README

          
[![Build Status](https://travis-ci.org/seqan/vaquita.svg?branch=master)](https://travis-ci.org/seqan/vaquita)



[Vaquita](http://www.worldwildlife.org/species/vaquita) accurately identifies __structural variations__ using split-reads, discordant read-pairs, soft-clipped reads, and read-depth information. Vaquita does not depend on external tools and very fast. You can analyze __50x WGS sample within an hour__.

Download & Compile

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

    git clone https://github.com/seqan/vaquita.git

    mkdir vaquita-build && cd vaquita-build

    cmake ../vaquita && make vaquita -j 4

Vaquita supports `GCC≥4.9` and `Clang≥3.8`.

Usage

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

    vaquita call -r [reference.fa] [input.bam] > [output.vcf]

The `.bam` file must be sorted by coordinate (eg. `samtools sort`).

You can find more options using `vaquita call --help`.

Citation

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

Jongkyu Kim and Knut Reinert, Vaquita: Fast and Accurate Identification of Structural Variations using Combined Evidence. _Workshop on Algorithmic Bioinformatics (WABI) 2017_

DOI: [10.4230/LIPIcs.WABI.2017.13](http://drops.dagstuhl.de/opus/volltexte/2017/7635/)

* You can find all the scripts and information about raw datasets that I used for benchmarking at [this repository](https://github.com/xenigmax/vaquita_WABI2017).

Contact

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

Jongkyu Kim (vaquita@jongkyu.kim)