TRGT-denovo v0.2.1

Summary of changes:

• 0.2.1
  • Duo and trio mode now always output entries regardless of error status (e.g., missing genotyping, skip because of quick mode). Missing column values are denoted by ., for instance if genotyping is missing in one sample, genotyping related information will still be output for the samples that did get genotyped.
  • Add denovo_status analog to duo mode. This has three possible states: {., X, Y:?}.

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.

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.

TRGT-denovo v0.1.2

Summary of changes:

• 0.1.2
  • With the recent changes to TRGT, within-sample partitioning is now alignment-free in TRGT-denovo
  • Homozygous alleles are no longer collapsed: de novo evidence will now always gathered and be specific to a single allele only
• 0.1.1
  • Add cli parameter to set aligner penalties
  • Document the codebase
  • Update documentation to include interpretation of generated output

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.

TRGT-denovo v0.1.0

This is the initial release of TRGT-denovo.

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.