使用说明书: https://github.com/xjtu-omics/msisensor-pro/blob/master/docs/4_command.md
首先扫描参考基因组获取参考基因组的msi区域
conda activate msisensor-pro
msisensor-pro scan -d gencode_GRCh38.p14.genome.fa -o gencode_GRCh38.p14.genome.msisensorpro.scan.regions接着构建WES运行msi的脚本
perl -ne 'chomp; next if /^$/; @a = split /\t/; print "msisensor-pro msi -d /data02/zhangmengmeng/database/hg38/gencode_GRCh38.p14.genome.msisensorpro.scan.regions -n ../align/$a[1]_bqsr.bam -t ../align/$a[0]_bqsr.bam -o $a[0] -c 20 && echo $a[0] msisensor-pro ok\n"' sample_pair.txt > RunMsiSensorPro.sh