TwiMM

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💬 Introduction

TwiMM is a bioinformatic pipeline designed to analyse hybrid capture long-read (PacBio HiFi) sequencing data from the multiple myeloma gene panel. It detects SNVs/InDels, structural variants (SV), and copy number variants (CNV). SV calling uses three callers in parallel (Severus, PBSV, Sniffles2) whose outputs are merged and annotated with population frequencies via SVDB.

❗ Dependencies

All dependencies are managed by pixi. Install pixi, then run:

pixi install

This resolves and installs all required packages (Python, Snakemake, hydra-genetics, and other tools) as defined in pixi.toml. Container images for individual pipeline tools are pulled automatically at runtime via Singularity/Apptainer and are listed in config/config.yaml.

🎒 Preparations

Sample data

Input data should be added to samples.tsv and units.tsv. The following information need to be added to these files:

Column Id	Description
samples.tsv
sample	unique sample/patient id, one per row
units.tsv	processed and raw BAM files should be in separate units files
sample	same sample/patient id as in samples.tsv
type	data type identifier (one letter), can be one of Tumor, Normal
platform	type of sequencing platform, e.g. PACBIO
machine	specific machine id, e.g. Revio
processing_unit	?
barcode	sequence library barcode/index or any character string, but not NA
methylation	Yes/No
bam	path to BAM file

✅ Testing

The pipeline uses pixi for environment management. Run a test dry-run locally:

pixi run test-dry

A small test dataset is also available in .tests/integration/.

🚀 Usage

# Dry run
pixi run all-dry

# Full run (SLURM cluster)
pixi run all-full

Refer to snakemake docs for advanced usage.

Output files

Key output files (see full list):

File	Description
results/snv_indels/{sample}_T.phased.include.panel.vep_annotated.vcf.gz	Phased SNVs/InDels annotated with VEP
results/cnv_sv/svdb_query/{sample}_T.vcf	Merged SVs annotated with population frequencies
results/cnv_sv/cnvkit_vcf/{sample}_T.pathology.annotate_cnv.germline.vcf	Annotated CNVs
results/reports/html/{sample}_T.pathology.cnv_report.html	Interactive CNV HTML report
results/xlsx_reports/{sample}_T_combined_report.xlsx	Excel report (SNV, SV, CNV + Software Versions)

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