https://github.com/illumina/reviewer
A tool for visualizing alignments of reads in regions containing tandem repeats
https://github.com/illumina/reviewer
Last synced: about 2 months ago
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A tool for visualizing alignments of reads in regions containing tandem repeats
- Host: GitHub
- URL: https://github.com/illumina/reviewer
- Owner: Illumina
- License: gpl-3.0
- Created: 2020-12-10T22:57:10.000Z (over 4 years ago)
- Default Branch: master
- Last Pushed: 2023-12-19T20:13:19.000Z (over 1 year ago)
- Last Synced: 2025-03-24T07:07:21.289Z (2 months ago)
- Language: C++
- Homepage:
- Size: 167 MB
- Stars: 83
- Watchers: 13
- Forks: 13
- Open Issues: 30
-
Metadata Files:
- Readme: README.md
- License: LICENSE.txt
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README
# Repeat Expansion Viewer (REViewer)
REViewer is a tool for visualizing alignments of reads in regions containing
tandem repeats. REViewer requires a BAMlet with graph-realigned reads generated
by [ExpansionHunter](https://github.com/Illumina/ExpansionHunter) and the
corresponding variant catalog.
## License
REViewer is provided under the terms and conditions of the [GPLv3 license](LICENSE.txt).
It relies on several third party packages provided under other open source licenses,
please see [COPYRIGHT.txt](COPYRIGHT.txt) for additional details.
## Installation
The simplest way of obtaining REViewer is by downloading a Linux binary
corresponding to the latest release from the
[Releases page](https://github.com/Illumina/REViewer/releases). The link to the
binary is located in the *Assets* section.
REViewer can also be built from source with CMake.
```shell script
cd REViewer
mkdir build; cd build
cmake ..; make
```
## Usage
REViewer requires output files generated by [ExpansionHunter](https://github.com/Illumina/ExpansionHunter)
v3.0.0 or above along with the
[matching variant catalog](https://github.com/Illumina/ExpansionHunter/blob/master/docs/04_VariantCatalogFiles.md)
file and reference genome.
```shell script
REViewer \
--reads \
--vcf \
--reference \
--catalog \
--locus \
--output-prefix
```
Note that the BAMlet generated by ExpansionHunter (`--reads` parameter) must be
sorted and indexed.
## Introductory guides
- [A blog post describing the method](https://www.illumina.com/science/genomics-research/reviewer-visualizing-alignments-short-reads-long-repeat.html)
- [Examples of read pileups](docs/examples.md) corresponding to correctly and
incorrectly genotyped repeats.
- You can use the files under `/reviewer/tests/inputs/` to test REViewer on your own machine.
(Don't use the outputs from the ExpansionHunter repository example; it contains variant locus
features that REViewer does not support, and will crash REViewer.)
## Reference documentation
- [Overview of the method and its limitations](docs/method-overview.md)
- [Description of the quality metrics reported by REViewer](docs/metrics.md)
## Companion tools
- [FlipBook](https://github.com/broadinstitute/flipbook) is an image server for
REViewer developed by [Ben Weisburd](https://github.com/bw2). It provides a
convenient way to inspect large quantities of read pileups.
- [Review BAMs](https://gitlab.com/andreassh/review-bams) is script that allows
applying REViewer to a regular BAM file (by running ExpansionHunter in the
background). It was developed by [Andreas Halman](https://gitlab.com/andreassh).
## Citation
- Dolzhenko E, Weisburd B, Garikano K, Rajan Babu IS, and colleagues,
[REViewer: Haplotype-resolved visualization of read alignments in and around
tandem repeats](https://www.biorxiv.org/content/10.1101/2021.10.20.465046v1),
bioRxiv, 2021