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Published November 17, 2023 | Version v1.9.0
Software Open

epi2me-labs/wf-human-variation: v1.9.0

Authors/Creators

  • 1. @nanoporetech
  • 2. Oxford Nanopore Technologies
  • 3. @Birkbeck
  • 4. @LooseLab

Description

Added

  • STR workflow report now includes additional plots which display repeat units and interruptions in each supporting read
  • CNV workflow now outputs an indexed VCF file to the output directory

Changed

  • Legend symbols in STR genotpying plot
  • Unambiguous naming of bedMethyl files generated with --mod
    • Unphased outputs will have the pattern [sample_name].wf_mods.bedmethyl.gz
    • Phased outputs will have the pattern [sample_name]_[1|2|ungrouped].wf_mods.bedmethyl.gz

Fixed

  • Report step failing if bcftools stats file has only some sub-sections
  • Clair3 ignoring the bed file
  • merge_haplotagged_contigs incorrectly generating intermediate CRAM when input is BAM
  • STR content generation failing due to forward slash in disease name in variant_catalog_hg38.json
  • Report name for the read alignment statistics now follows the pattern [sample_name].wf-human-alignment-report.html

Files

epi2me-labs/wf-human-variation-v1.9.0.zip

Files (2.2 MB)

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md5:e5118605cd754dcdbb05caeb80c2c1b3
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Additional details

Related works

Is supplement to
Software: https://github.com/epi2me-labs/wf-human-variation/tree/v1.9.0 (URL)

Software

Repository URL
https://github.com/epi2me-labs/wf-human-variation