TRGT-denovo v0.2.0

Summary of changes:

• 0.2.0

  • Implemented duo mode, it is now possible to perform 1-to-1 sample comparisons, following the same principles as in trio analysis. This can be done using the subcommand trgt-denovo duo.
  • Implemented the --quick flag. Users can now specify --quick AL[,<fraction>] to skip loci where allele lengths are similar between parents and child or between two samples. If no fraction is specified (or fraction is 0), it checks for exact matches. If a fraction is specified, it checks if the relative difference is within the given tolerance.
  • Added a Jupyter notebook in scripts/python/trio_analysis.ipynb to describe a simple trio analysis to do de novo candidate selection.

• 0.1.3

  • Changes to TRGT-denovo output:
    • Truncate zeros in output.
    • Report TRGT allele lengths observed in each family member as sample_AL.
    • Renamed TRGT motif counts from sample_motif_counts to sample_MC.
    • Report the overlap coverage; this is the reciprocal of the de novo coverage, i.e., the number of reads in per allele in the parent that overlap compared to the child data.
  • Lower memory footprint: Better memory management, significantly reduces memory usage with large repeat catalogs.
  • Improved IO error handling.

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

Linux binaries are available below.