Changelog

v2.5.3-dev

  • Fix a typo in the default configuration where the rare RARA fusion partner STAT3 was written as STAT3B. Note that the impact should be minimal since all fusions with RARA are reported when using the default configuration.

v2.5.2

  • Important: Please rebuild the HAMLET-data folder when updating to v2.5.2

  • Update variant annotation and inclusion criteria

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

v2.1.0

  • Breaking change: Remove the JSON output for the qc-seq module (this has been replaced by a MultiQC report)

  • Breaking change: Add sample name to STAR counts table * Fix a bug where the trimmed FastQ files are not removed when no longer needed

  • Automatically remove _STAR temporary folders

  • Change PDF report cover image

  • Change PDF report to add bookmarks under chapter variant

  • Change PDF report to sort the genes of interest alphabetically

  • Change PDF report to remove the “Sequencing Results” section (this has been replaced by a MultiQC report)

  • Replace FastQC with Sequali

  • Update Cutadapt to 4.6

  • Update MultiQC to 1.22

  • Update snakefmt to 0.10.0 (developer only)

  • Update black to 24.3.0 (developer only)

v2.0.5

  • Change PDF report to increase space for the HGVS description in “Results Overview” table

v2.0.4

  • Automatically check the release tag is set correctly

v2.0.3

  • Fix a bug where long HGVS descriptions make the “Results Overview” table overflow the page

v2.0.2

  • Include the sample name in the final BAM file

v2.0.1

  • Update version number in HAMLET report

v2.0.0

  • Breaking change: Deprecate option fusion-partners, in favour of report_genes, which points to a list of fusion genes to report

  • Fix a bug with inconsistent config setting blacklist in snv-indels

  • Fix a bug where unmapped reads are not included in STAR output file

  • Replace StarFusion and FusionCatcher with Arriba

  • Replace VarScan variant caller with VarDict

  • Replace GSNAP aligner with STAR

  • Update VEP to 108.2

  • Update Picard to 2.27.4

  • Update FastQC to 0.11.9

  • Update Cutadapt to 4.1

  • Change PDF report to remove the run name

  • Change PDF report to remove variants plots

  • Change PDF report to show allele frequency as a percentage

  • Use multiple threads for Cutadapt, and reduce the compression of output files

  • Add additional genes of interest

    • SRSF2

    • SF3B1

    • U2AF1

    • BCOR

    • STAG2

    • ZRSR2

    • EZH2

  • Filter fusion results based on fusion partners

  • Add fusion plots from Arriba

  • Add default blacklist with common false-positive variants

  • Add support for variant blacklist in VEP hgvsc format

  • Add script to generate a configuration file

  • Add pipeline to generate reference files

  • Add per-module configuration options

  • Add support for PEP sample configuration

  • Add support for Snakemake 7.8.5

  • Use MANE select transcript for all genes