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

#inputpath=$1
#sample=$2
source  /home/liuxiangqiong/miniconda3/bin/activate base
target=/cgdata/liuxiangqiong/work62pancancer/pipeline/v0/refdata/NanOnco_Plus_Panel_v2.0_Covered_b37_cg.parY2X.sort.bed
ourputdir=${inputpath}/9Ontarget
samtools flagstat ${bam_dir}/${sample}_clean.bam > ${ourputdir}/${sample}_clean.abra2.flagstat
cd ${ourputdir}
qualimap bamqc -bam  ${bam_dir}/${sample}_clean.bam  -c --java-mem-size=40G -gff ${target}