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