Xiao198/SpotSV

SpotSV：a SV Validation Tool

运行环境

Linux

所需依赖包

python3 pysam bcftools matplotlib os math random time signal shutil

进入src文件夹

cd SpotSV/src

运行提示命令

python spotsv.py valid -h

根据提示命令输入文件即可运行

usage: spotsv.py valid [-h] -s SV_INPUT -o OUT_PATH -r REF_PATH -b BAM_INPUT [-t THREADS] [-p] --data_type {CCS,ONT,CLR}

optional arguments: -h, --help show this help message and exit -s SV_INPUT path to input file in bed or vcf format -o OUT_PATH path to output -r REF_PATH path to ref -b BAM_INPUT path to bam -t THREADS thread number -p whether to output processing images --data_type {CCS,ONT,CLR} data type, choose from CCS,ONT and CLR