- #!/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}
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