v2.5.1

• Fix a bug with the HAMLET-data folder

v2.5.0

• Important: Please rebuild the HAMLET-data folder when updating to v2.5.0
• Deprecate the blacklist option in favour of known_variants
• Deprecate the ref_id_mapping option
• Deprecate the vep_include_consequence option
• Rename filter_criteria to inclusion_criteria
• Add option min_variant_depth to the snv-indels module to specify the
  minimum number of reads to report a variant (default = 2)
• Add support for specifying the frame of variant Criteria
• Add additional annotation file known_variants to the snv-indels module
• Add the --safe flag to VEP to ensure there are no hidden errors
• Add support for tabulating gene expression data to the hamlet_table.py script
• Add support for tabulating cell types to the hamlet_table.py script
• Add support for tabulating AML subtype prediction to the hamlet_table.py script
• Simplify the output of the hamlet_table.py script for variants
• Allow every module to run with the full HAMLET configuration
• The report_genes file for the fusion module is now optional
• Encode all figures directly into the HTML report
• Clean up intermediate MultiQC files
• Truncate HGVS descriptions longer than 100 characters in the PDF report
• Combine filtering and annotation of variants into a single step
• Update the filter and annotation criteria to include 46 genes
• Reduce the size of the reference files to 35GB
• Update MultiQC to 1.31
• Update cutadapt from 5.0 to 5.1
• Update sequali from 0.12 to 1.0.2
• Update arriba from 2.4.0 to 2.5.1
• Update VEP from 108 (2022) to 115 (2025)

v2.4.0

• Fix a bug in the dependency pipeline introduced by Snakemake 8
• Fix a bug with the cell type composition in MultiQC
• Add seAMLess to determine cell type composition
• Add section for gene expression to the PDF report
• Add seAMLess cell type composition to PDF and MultiQC report
• Add Picard Strand Mapping statistics to the MultiQC report
• Add AML subtype prediction with AMLmapR
• Add seAMLess reference files to HAMLET-data
• Add hotspot criteria file to HAMLET-data
• Remove table and figure numbers from the PDF report

v2.3.3

• Add script to update HAMLET version (developer)
• Rename the PDF manual in the release bundle
• Add example HAMLET report to the release bundle
• Add example MultiQC report to the release bundle

v2.3.2

• Automatically create release notes from Changelog

v2.3.1

• Breaking change: Removed bed_variant_hotspots in favor or annotation_criteria
• Breaking change: Variants are now filtered using the filter_criteria file
• Breaking change: Add mutalyzer_hgvs_parser to the conda environment
• Breaking change: Update the json output format
• Breaking change: Update Snakemake to version 8
• Fix a bug with the Java runtime environment for Picard
• Fix a bug with caching of report assets introduced in snakemake 8
• Fix a bug with structural variants missing effect prediction
• Add an option to specify variant_allele_frequency for snv-indels
• Speed up VarDict by running with 8 threads
• Speed up VarDict by sorting the call_regions.bed file
• Run VEP with either vep_cache or just the gtf/fasta files as database
• Update picard from 2.27.4 to 3.3.0
• Update cutadapt from 4.6 to 5.0
• Update sequali from 0.9.1 to 0.12.0
• Update star from 2.7.10b to 2.7.11b
• Update MultiQC to 1.27.1

v2.2.1

• Breaking change: The bed_variant_call_regions option has been removed, variants are now
  called for all genes present in the gtf file.
• Breaking change: Add graphviz/dot as a dependency (developer only).
• Fix a rare bug where different modules use the same MultiQC file list.
• Fix a bug with filtering VEP records that contain multiple population.
  frequency records for a single variant.
• Add ability to generate configurations for each module using the
  utilities/create-config.py script.
• Update the hotspot regions reference file.
• Update the blacklist of known artifacts.
• Remove various superfluous plots from the MultiQC report.
• Add expression module
  • Add optional input strandedness to the sample configuration.
  • Add json output file for the expression module.

v2.1.3

• Add pysam to the conda environment (developer only)
• Add exon number to variant table
• Add chromosomes to fusion table

v2.1.2

• Fix a bug with the maximum population frequency, this was accidentally set to
  5% (it is now 1%)

v2.1.1

• Fix a bug where VEP removed rare variants