Changelog

v2.2.1

Breaking changes

  • The bed_variant_call_regions option has been removed, variants are now called for all genes present in the gtf file.

  • Add graphviz/dot as a dependency (developer only).

  • Please create a new HAMLET configuration file with create-config.py script.

  • To use the latest hotspot regions and artifact blacklist, please recreate the HAMLET reference data.

Novel module

  • Add novel module, expression, which analyzes gene expression. * Add optional input strandedness to the sample configuration. * Add json output file for the expression module.

Bugfixes

  • 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.

Updates

  • 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.

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

  • Set the maximum population frequency to 1%. This was accidentally set to 5% in v2.1.1

v2.1.1

Bugfixes

  • Fix a bug where VEP removed rare variants

v2.1.0

Breaking changes

  • Remove the JSON output for the qc-seq module (this has been replaced by a MultiQC report)

  • Add sample name to STAR counts table

Changes

  • Automatically remove _STAR temporary folders

  • Modified PDF formatting * Change cover image * Add bookmarks under chapter variant * Sort the genes of interest alphabetically * Lock snakefmt version * Remove the “Sequencing Results” section from the report (this has been replaced by a MultiQC report)

  • Replace FastQC with Sequali

Bugfixes

  • Fix a bug where the trimmed FastQ files are not removed when no longer needed

Updates

  • 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

  • Increase space for the HGVS description in “Results Overview” table

v2.0.4

  • Automatically check the release tag is set correctly

v2.0.3

Bugfixes

  • 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

Bugfixes

  • Update version number in HAMLET report

v2.0.0

Bugfixes

  • Fix a bug with inconsistent config setting ‘blacklist’ in snv*indels

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

Tool changes

  • Replace StarFusion and FusionCatcher with Arriba

  • Replace VarScan variant caller with VarDict

  • Replace GSNAP aligner with STAR

Tool updates

  • Update VEP to 108.2

  • Update Picard to 2.27.4

  • Update FastQC to 0.11.9

  • Update Cutadapt to 4.1

Speed improvements

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

Changes

  • Remove run name from the report

  • Deprecate option fusion*partners, in favour of report_genes, which points to a list of fusion genes to report

  • Show allele frequency as a percentage in the pfd report

  • 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

  • Remove variants plots

  • Use MANE select transcript for all genes