- 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).
- Add novel module, expression, which analyzes gene expression * Add optional input strandedness to the sample configuration * Add json output file for the expression module
- Fix a rare bug where different modules use the same multiqc file list
- Add pysam to the conda environment (developer only)
- Add exon number to variant table
- Add chromosomes to fusion table
- Set the maximum population frequency to 1%. This was accidentally set to 5% in v2.1.1
- Fix a bug where VEP removed rare variants
- Remove the JSON output for the qc-seq module (this has been replaced by a MultiQC report)
- Add sample name to STAR counts table
- 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of interest alphabetically * Lock snakefmt version * Remove the "Sequencing Results" section from the report (this has been replaced by a MultiQC report)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
- Fix a bug where the trimmed FastQ files are not removed when no longer needed
- 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)
- Increase space for the HGVS description in "Results Overview" table
- Automatically check the release tag is set correctly
- Fix a bug where long HGVS descriptions make the "Results Overview" table overflow the page
- Include the sample name in the final BAM file
- Update version number in HAMLET 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
- Use multiple threads for Cutadapt, and reduce the compression of output files
- 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