FeaturesΒΆ

  • built-in support for:
    • translocations (new feature!)
    • deletions
    • insertions
      • including mobile element insertions
      • complex insertions (where some sequence is deleted)
    • inversions
    • svviz can easily be extended to analyze translocations and complex variants, but these types are not yet implemented.
  • builds reference and alternate allele sequences from genome fasta file and structural variant annotation
  • identifies, from the input bam file(s), which reads (both read ends for paired-end sequencing) are likely to be relevant for the given structural variant
  • performs Smith-Waterman realignment of all read segments against both alternate and reference allele sequences
  • uses alignment score to determine reads supporting reference or alternate allele
  • additionally, uses empirical insert-size distribution (rather than mean and stddev) to assign reads as likely derived from alternate or reference allele
  • provides a (locally-running) browser-based front-end for inspecting visualizations
  • visualizes reads for multiple samples in SVG format (an open-source, web-standard vector graphics format)
    • shows mismatched bases indicative of sequence polymorphisms (eg SNPs) or mapping errors
    • can visualize BED or GTF format annotations, for example the locations of genes or repeats
  • optionally visualizes repetitiveness in the breakpoint regions using dotplots
  • options to export to PDF or PNG
  • batch mode to calculate summary statistics and create visualizations for many events from a VCF file