TRGT v3.0.0

Summary of changes:

• Breaking change: Modified how TRGT detects repeat motifs
  • Repeat segmentation algorithm only matches perfect STR motifs (imperfections in VNTR motifs are still allowed)
  • More flexible motif matching that allows better detection and visualization of repeat interruptions
• Made a number of improvements to TRGT plots
  • The size scale is replaced with the overall allele length
  • More accurate motif matching in waterfall plots
  • Similar alignments are grouped together
  • The plots can be compressed vertically (useful for high-depth targeted data)
  • Easier to distinguish between mismatches and unsegmented regions
• Bug fix: Explicitly set reference from genome path for CRAM input, avoiding issues with moved/renamed references (thanks to @Han-Cao for reporting and @ASLeonard for suggesting a solution)

Notes
This release introduces significant changes to the repeat segmentation algorithm. While the previous versions of TRGT allow imperfections in both STR (<=6bp) and VNTR (>6bp) motifs, the new algorithm requires all STR motif matches to be perfect (imperfections in VNTR motifs are still allowed). For example, the allele CAG⋅CAG⋅CAG⋅CAA⋅CAG⋅CAG⋅CAG would have been previously reported to contain 7 CAGs (6 perfect copies and 1 imperfect copy). Now it is reported to contain 6 CAGs.

Contributors: Tom Mokveld, Guilherme De Sena Brandine, and Egor Dolzhenko

Note: TRGT is still in active development. Please file an issue or reach out by email with questions, bug reports, and feature suggestions.

Linux binary is available below.