#!/bin/sh
#PBS -N MSIpair_15R_msisensor2
#PBS -j oe
#PBS -l ncpus=12
#PBS -l nodes=1
#PBS -l mem=20G


source  /home/liuxiangqiong/miniconda3/bin/activate base
outputdir=${inputpath}/3MSI_msisensor2_pair
msisensor2 msi  -d /cgdata/liuxiangqiong/work62pancancer/pipeline/v0/refdata/MSI_15.slop50.msisensor.b37.str.tsv -n ${bam_dir}/${normal}_clean.bam -t ${bam_dir}/${tumor}_clean.bam -o ${outputdir}/${sample}.15STR