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@pdimens pdimens released this 24 Aug 19:02
· 1390 commits to main since this release
0.3.0
c333c85
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Learn about vigilant mode.

New features

  • freebayes variant calling
  • naibr variant calling
  • bam filename/RG tag validations
  • unit testing (not relevant for end-user)
  • --vcf-samples options for impute and phase
  • file/vcf sample validations
  • STITCH parameter file validations
  • genome assembly bgzipping validation/handling
  • much more flexible regex for fastq filenames
  • STITCH param file column order no longer matters and is not case-sensitive
  • new demultiplex module for Generation I (Meier et al., 2022) haplotag beads

Breaking changes

  • snp and sv variant calling now split into separate submodules under variants
    • variants --method is now variants snp --method and variants sv --method
  • STITCH param file has extra column bxlimit
  • the validations listed above will force Harpy to terminate if errors are detected
  • folder structure for output of align slightly different

Non-breaking changes

  • added Snakemake --nolock and --rerun-incomplete flags to all workflows
  • all workflows now provide appropriate exit codes
  • snp variant calling now occurs by genomic interval rather than by contig (a lot more parallel, a lot faster)
  • EMA aligns all preproc files at once into single alignment file, rather than aligning each individually and merging after
  • samtools stats/flagstat reports combined into single report
  • phase reports reworked/rewritten
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