Twitcher Documentation

Twitcher is a tool for re-annotating VCF files and identifying template switch mutations in genomic data.

• Installation: Install Twitcher (prebuilt binary or from source)
• Usage: Run Twitcher on your data
• Concepts: Understand template switches, the vcf and reads modes, and realignment
  • Aligners: The A* and four-point aligners and their properties
  • Clustering: How mutations are grouped into clusters
  • Phasing: Read-based phasing of ambiguous VCF clusters
  • Database: Caching and reusing alignments
• Key Parameters: The most important parameters and switches
  • CLI Reference: All command line arguments
• Output Files: The files Twitcher writes
  • CSV Output: The most important columns
  • TSIGAR Format: Encoding of template switch events
  • Alignment Statistics: Runtime, memory and provenance for every alignment
• Cost Model: Understand the cost function