MShunter

MSHunter is still in development. Please report bugs via GitHub issues.

If you have any question about this software, please contact with Peng Jia (pengjia@stu.xjtu.edu.cn)

Installation

git clone https://github.com/microsatellites/MSHunter.git
cd MSHunter
mamba env create -f ./mshunter_env.yaml
conda activate mshunter_env
python setup.py
mshunter -h 

Quik start

 mshunter genotype  -m GRCh38_noSimpleRepeat_chr1.list  -i HG00731.ILM.GRCh38.bam -r GRCh38_full_analysis_set_plus_decoy_hla.fa -o output_test -tech ilm  -t 20 

parameters:

• -m: microsatellite files, generated by scan module of msisensor-pro (see example)
• -i aligned bam file or cram file
• -r reference file
• -o output directory
• -tech sequencing technology
• -t threads used