Changelog

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