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- #!/bin/sh
- #PBS -N igv_report
- #PBS -j oe
- #PBS -l ncpus=20
- #PBS -l nodes=1
- #PBS -l mem=20G
- source /home/liuxiangqiong/miniconda3/bin/activate base
- ##获得igv输入数据
- python3 /cgdata/liuxiangqiong/work62pancancer/Client/v0/script/20220705/igv_input.py -i ${inputpath} -s ${sample}
- #inputpath=/cgdata/bioproject/pancancer602gene/CAP2022
- hg19=/cgdata/Database/GATK/hg19/ucsc.hg19.fasta
- ##获得laneid
- array=(${inputpath//\// })
- lenth=${#array[*]}
- laneid=${array[lenth-1]}
- outputir=${inputpath}/tempfile/igv
- ###对于somatic
- bamdir_tumor=${bam_dir}/${tumor}_clean.bam
- create_report ${outputir}/${laneid}-${sample}.snv.txt ${hg19} \
- --ideogram /cgdata/liuxiangqiong/software/igv-reports/igv-reports-master/test/data/hg19/cytoBandIdeo.txt \
- --flanking 1000 \
- --sort BASE \
- --sequence 1 --begin 2 --end 3 \
- --flanking 1000 \
- --info-columns Chr Start End Ref Alt Gene.refGene Transid_uniq ExonicFunc.refGene VAF_tumor DP_tumor VD_tumor DP_normal VD_normal VAF_normal sampleid \
- --tracks ${bamdir_tumor} /cgdata/liuxiangqiong/work62pancancer/igv-report/refGene.txt.gz \
- --output ${outputir}/${laneid}-${sample}.snv.html
- #对于germline
- bamdir_normal=${bam_dir}/${normal}_clean.bam
- create_report ${outputir}/${laneid}-${sample}.germline.txt ${hg19} \
- --ideogram /cgdata/liuxiangqiong/software/igv-reports/igv-reports-master/test/data/hg19/cytoBandIdeo.txt \
- --flanking 1000 \
- --sort BASE \
- --sequence 1 --begin 2 --end 3 \
- --flanking 1000 \
- --info-columns Chr Start End Ref Alt Gene.refGene AAChange_select ExonicFunc.refGene VAF N_ref N_alt sampleid \
- --tracks ${bamdir_normal} /cgdata/liuxiangqiong/work62pancancer/igv-report/refGene.txt.gz \
- --output ${outputir}/${laneid}-${sample}.germline.html
- #删除中间文件
- rm -rf ${outputir}/${laneid}-${sample}.snv.txt
- rm -rf ${outputir}/${laneid}-${sample}.germline.txt
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