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)
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 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