wally

Render BAM/CRAM alignments in the web browser.

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How to use wally

              
Local BAM/CRAM files

              
    
                
  1. Drag one or more sorted, indexed BAM/CRAM files and their .bai/.crai indexes into the drop zone.
    2. 
                
  2. Add a matching reference FASTA and its .fai (and .gzi if the reference is bgzipped).
    3. 
                
  3. Optionally add a bgzipped, tabix-indexed BED annotation (.bed.gz + .tbi) to overlay, for instance, gene models.
    4. 
                
  4. Enter a region and click Render Region.
    5. 
              

              
Remote 1000 Genomes data

              
    
                
  1. Pick a reference build (GRCh38 or T2T-CHM13) and add one or more samples.
    2. 
                
  2. Enter a region and click Render Region.
    3. 
              

              

                On the Results tab you can zoom, shift, and pan the plot, toggle tracks (paired-end,
                soft-clips, supplementary, coverage, genes, modified bases), and set the row height with the slider.
		Click Show Example for a bundled demo.
              

              

                Everything runs locally via WebAssembly, i.e., local BAM/CRAM files never leave your computer.