- #!/bin/sh
- #PBS -N damage
- #PBS -j oe
- #PBS -l ncpus=40
- #PBS -l nodes=1
- #PBS -l mem=50G
- source /home/liuxiangqiong/miniconda3/bin/activate base
- bam_dir=/cgdata/pancancer/analyse/${laneid}/bamfile
- #tumor=Lib51623TTT
- outputdir=/cgdata/bioproject/pancancer602gene/${laneid}/tempfile/QC
- fgbio=/cgdata/liuxiangqiong/software/fgbio/fgbio-1.3.0.jar
- ref=/cgdata/Database/GATK/b37/human_g1k_v37_decoy.fasta
- target=/cgdata/liuxiangqiong/work62pancancer/pipeline/v0/refdata/NanOnco_Plus_Panel_v2.0_Covered_b37_cg.parY2X.sort.bed
- dbsnp138=/cgdata/Database/GATK/b37/dbsnp_138.b37.vcf
- java -jar $fgbio ErrorRateByReadPosition -i ${bam_dir}/${tumor}_clean.bam --collapse=false -r $ref -v $dbsnp138 -o $outputdir/$tumor
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