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- #!/bin/sh
- #PBS -N CNVpair_cnvkit
- #PBS -j oe
- #PBS -l ncpus=12
- #PBS -l nodes=1
- #PBS -l mem=20G
- #inputpath=$1
- #sample=$2
- source /home/liuxiangqiong/miniconda3/bin/activate base
- hg19=/cgdata/Database/GATK/b37/human_g1k_v37_decoy.fasta
- target=/cgdata/liuxiangqiong/work62pancancer/pipeline/v0/refdata/NanOnco_Plus_Panel_v2.0_Covered_b37_cg.parY2X.sort.bed
- includhg19=/cgdata/liuxiangqiong/database/cnvkit/data/access-5k-mappable.grch37.bed
- outputdir=${inputpath}/2CNV_cnvkit_pair
- cnvkit.py batch \
- ${bam_dir}/${tumor}_clean.bam \
- --normal ${bam_dir}/${normal}_clean.bam \
- --targets ${target} \
- --fasta ${hg19} \
- --access ${includhg19} \
- --output-reference ${outputdir}/${normal}_my_reference.cnn \
- --output-dir ${outputdir}/${sample}_cnvkit/ \
- --diagram --scatter
- ###extract the cnr data for multi-region of gene
- python3 /cgdata/liuxiangqiong/work62pancancer/pipeline/v0/noUMI_v0/cnvkit_cnr_gene20220525.py -i ${inputpath} -s ${sample} -t ${tumor}
- ####do the cnvkit segment for the multi-region gene
- cnvdir=${inputpath}/2CNV_cnvkit_pair/${sample}_cnvkit
- cat ${cnvdir}/${tumor}_seggene.list |while read gene;do cnvkit.py segment ${cnvdir}/${tumor}_${gene}_gene.cnr -o ${cnvdir}/${tumor}_${gene}_gene.seg.cns --smooth-cbs;done
- ###merge the cns data
- #python3 /cgdata/liuxiangqiong/work62pancancer/pipeline/v0/noUMI_v0/cnvkit_cns_merge_20220525.py -i ${inputpath} -s ${sample} -t ${tumor}
- python3 /cgdata/liuxiangqiong/work62pancancer/pipeline/v0/noUMI_v0/cnvkit_cns_merge_20220823.py -i ${inputpath} -s ${sample} -t ${tumor}
- #del the file
- rm -rf ${cnvdir}/*gene.seg.cns
- rm -rf ${cnvdir}/*gene.cnr
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