mutsuite

A framework for simulating, calling, and benchmarking indel and structural variant detection in whole genome sequencing (WGS) data.

Features

• mutSim: Simulate indels and other mutations in BAM files
• mutRun: Orchestrate the running of many mutations with varying mutation parameters
• mutTest: Run multiple variant callers (Pindel, Mutect, Lofreq, Strelka, SomaticSniper, Vardict, Varscan, and more)
• mutAgg: Aggregate and compare results from different callers

Directory Structure

• docs/ — Example analysis scripts and notebooks
• src/ — MutSim source code

Getting Started

1. Clone the repository
2. Set up the environment
   • Use the provided conda.env file to create a conda environment:

     conda create -n mutsuite --file docs/conda.tx
     conda activate mutsuite

3. Configure your simulation
   • Edit a settings file (see docs/simSettings.txt for an example)
4. Run the main notebook or scripts
   • Example: Open and run docs/demo.ipynb

Example Settings File

[Simulation]
depths: 30,100
pctMut: 0.05,0.1,0.15
addQual: 0
reps: 3
chr: chr2
loc: 72933869
simulateRange: 5000
FDRtolerance: 10,100,1000
reference: hg38/genome.fa
sourceBam: NA12878/HG001.GRCh38_full_plus_hs38d1_analysis_set_minus_alts.300x.bam
alteredBam: SRR1046762.bam
useOnlyIndels: True

Adding a New Caller

• Implement a new class inheriting from Caller (see callers/pindelCaller.py for an example)
• Add your caller to the list in the main notebook or script