v1.9.1

Changed

• ClinVar annotation of SVs has been temporarily removed due to not being correctly incorporated. SnpEff annotations are still produced as part of the final SV VCF.
• New documentation

Removed

• --annotation_threads parameter, as the SnpEff process does not support multithreading.

Fixed

• Truncated SV VCF header generated from vcfsort.
• sed crashing with I/O error in some instances.
• Missing flagstats file in output directory.

v1.9.0

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

v1.8.3

Fixed

• configure-jbrowse breaking on unescaped spaces

v1.8.2

Added

• The SNP workflow will filter the final VCF to only return calls in the regions specified with --bed
  • Avoid clair3 calling variants in regions that flank those specified in the BED

Fixed

• SNP subworkflow was ignoring BED file and analysing all regions
• Report SV crashing when generating the size plots with only large indels
• Downsampling not working when targeting regions with --bed
• --phase_mod not emitting the haplotagged bam files
• Report crashing when loading a clinvar-annotated VCF file with multiple GENEINFO/CLNVC entries

Removed

• Default local executor CPU and RAM limits

v1.8.1

Fixed

• SV size barchart causing extremely large reports.
  • The plot has been replaced with a distribution plot fixed to +/- 5KBp. The summary table reports the INS and DEL min/max values.
• Workflow could not be launched from EPI2ME desktop app due to incorrectly quoted fields in schema

v1.8.0

Changed

• replaced --methyl with --mod, and --phase_methyl with --phase_mod
• replaced modbam2bed with modkit (v0.1.12)
• --phase_mod will generate three bed files, one for each haplotype and one for the reads that are not tagged.

Added

• Add locus for LRP12 to BED file of STR repeats (GRCh38)

v1.7.2

Changed

• When --bed and --bam_min_coverage are specified, the workflow will process the regions passing the coverage filters
• whatshap v2.0 in base workflow

Fixed

• Patch whatshap stats crashing when no heterozygote sites are found in a contig
• Patch makeReport crashing when loading empty ClinVar VCFs

v1.7.1

Changed

• Increased minimum memory required for the workflow to 16 GB of RAM to reduce alignment failures

Fixed

• sv.filterBam missing output file when creating BAM CSI

v1.7.0

Changed

• VCFs generated by the --sv option are now automatically annotated with SnpEff, incorporating ClinVar annotations
  • This can be switched off with --skip_annotation
• —-skip_annotation disables attempt to determine human genome version, enabling --snp, --sv and --phase_methyl to be called on genomes which aren’t hg19 or hg38
• Updated example command displayed when running --help
• The ClinVar table in --snp and --sv reports is now sorted according to clinical significance, and includes HGVS cDNA and protein descriptions
• Workflow options for disabling steps have been updated for consistency:
  • --skip_annotation is now --annotation false
  • --skip_refine_snp_with_sv is now --refine_snp_with_sv false
• --phase_methyl also calls modifications using all reads to account for unphased regions
• Input options and Output options have been combined in the Main options category
• Updated Clair3 to v1.0.4
• SV workflow does not filter the SV calls by size and type
• Report for bam files failing the depth threshold is now consistent with the report of bam passing the hard threshold
• Perform Sniffles SV phasing with --phase_sv
• --phase_vcf now run Sniffles SV in phasing mode

Fixed

• 'mosdepth_downsampled' is defined more than once warning
• Workflow crashing when providing a reference with spaces/brackets in file name
• Workflow not emitting GVCF even when requested
• GVCF sample name not matching sample_name
• --cnv subworkflow sometimes reporting incorrect genetic sex, due to the way segment copy numbers were aggregated across chromosomes

Added

• Add downsampling of large bam files
• --joint_phasing allows an additional joint SNP and SV phasing
• --joint_phasing and --phase_vcf now emit a phased block GTF file to facilitate visualization

Removed

• --sv_types, all SV types are returned without filtering
• --max_sv_length, all SVs are returned regardless of maximum size

v1.6.1

Changed

• GPU tasks are limited to run in serial by default to avoid memory errors
  • Users in cluster and cloud environments where GPU devices are scheduled must use -profile discrete_gpus to parallelise GPU work
  • A warning will be printed if the workflow detects it is running non-local execution but the discrete_gpus profile is not enabled
  • Additional guidance on GPU support is provided in our Quickstart

Fixed

• ModuleNotFoundError on callCNV step when transforming some VCFs
• Malformed VCF created by annotation step if Java emits a warning