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 and the corresponding variant catalog.
REViewer is provided under the terms and conditions of the GPLv3 license. It relies on several third party packages provided under other open source licenses, please see COPYRIGHT.txt for additional details.
The simplest way of obtaining REViewer is by downloading a Linux binary corresponding to the latest release from the Releases page. The link to the binary is located in the Assets section.
REViewer can also be built from source with CMake.
cd REViewer mkdir build; cd build cmake ..; make
REViewer \ --reads <BAMlet generated by ExpansionHunter> \ --vcf <VCF file generated by ExpansionHunter> \ --reference <FASTA file with reference genome> \ --catalog <Variant catalog> \ --locus <Locus to analyze> \ --output-prefix <Prefix for the output files>
Note that the BAMlet generated by ExpansionHunter (
--reads parameter) must be
sorted and indexed.
- A blog post describing the method
- Examples of read pileups 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.)
- Dolzhenko E, Weisburd B, Garikano K, Rajan Babu IS, and colleagues, REViewer: Haplotype-resolved visualization of read alignments in and around tandem repeats, bioRxiv, 2021