v2.0.0

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.