v1.10.0

Added

• Clair3 4.3.0 models.

Changed

• --phase_vcf, --joint_phasing and --phase_mod are now deprecated for --phased; see the README for more details.
• --use_longphase_intermediate is now deprecated, and --use_longphase false will use whatshap throughout consistently
• Running --phase --snp --use_longphase false will now phase indels too
• --basecalling_cfg currently provides the configuration to Clair3.
• The clair3: prefix to Clair3 specific models is no longer required.

Fixed

• CNV report generation fails if there is no consensus on the copy number of a chromosome
  • Undetermined category has been added to the Chromosome Copy Summary to account for these cases
• readStats reports metrics on the downsampled BAM when --downsample_coverage is requested.
• Spurious warning for missing MM/ML tags when a BAM fails the coverage threshold

Removed

• wf-basecalling subworkflow
  • fast5_dir input and other basecalling related options have been removed from the workflow parameters
  • Users should run the standalone wf-basecalling workflow and provide the output to wf-human-variation
• Mapula statistics with --mapula