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Published March 6, 2024 | Version v2.0.0
Software Open

epi2me-labs/wf-human-variation: v2.0.0

Authors/Creators

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

Description

Changed

  • CNV calling with --cnv is now performed using Spectre, which is optimised for long reads.
    • Legacy CNV calling using QDNAseq may still be carried out with --cnv --use_qdnaseq.
    • The bin size parameter has been renamed from --bin_size to --qdnaseq_bin_size.
  • Skip CNV CRAM to BAM conversion if downsampling is required, to avoid creating an unnecessary intermediate file.
  • The output of --depth_intervals now has .bedgraph.gz extension.
  • SV workflow outputs SVs in the autosomes, sex chromosomes and MT; use --include_all_ctgs to output calls on all the sequences.

Added

  • Output definitions for coverage files.
  • N50 and mean coverage added to alignment report.

Fixed

  • EPI2ME Desktop incorrectly allowed selection of directory for tr_bed.
  • failedQCReport failing to generate a report.

Files

epi2me-labs/wf-human-variation-v2.0.0.zip

Files (2.2 MB)

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md5:8b7fc0e20374567666935b7831c6d202
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Additional details

Related works

Is supplement to
Software: https://github.com/epi2me-labs/wf-human-variation/tree/v2.0.0 (URL)

Software

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