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.

References:

• Dolzhenko E, Weisburd B, Garikano K, Rajan Babu IS, and colleagues,
  REViewer: Haplotype-resolved visualization of read alignments in and around tandem repeats
  bioRxiv,

• REViewer Home page

• Module Name: REViewer (see the modules page for more information)
• Unusual environment variables set

Allocate an interactive session and run the program. Sample session:

[user@biowulf]$ sinteractive --mem=10g -n 4
[user@cn3316 ~]$ module load REViewer
[+] Loading REViewer  0.2.7
[user@cn3316 ~]$ REViewer
Program options:
  --help                                Print help message
  --version                             Print version number
  --reads arg                           BAMlet generated by ExpansionHunter
  --vcf arg                             VCF file generated by ExpansionHunter
  --reference arg                       FASTA file with reference genome
  --catalog arg                         Variant catalog
  --locus arg                           Locus to analyze (or a list of
                                        comma-separated loci)
  --region-extension-length arg (=1000) Length of flanking region (must match
                                        corresponding ExpansionHunter setting)
  --output-prefix arg                   Prefix for the output files

[user@cn3316 ~]$ exit
salloc.exe: Relinquishing job allocation 46116226
[user@biowulf ~]$