602panel_test/s7_noUMI_fusion_GeneFuse_unpair_20220929.sh

#!/bin/sh
#PBS -N Genefusion
#PBS -j oe
#PBS -l ncpus=20
#PBS -l nodes=1
#PBS -l mem=30G

#inputpath=$1
#sample=$2
source  /home/liuxiangqiong/miniconda3/bin/activate base
hg19=/cgdata/Database/GATK/b37/human_g1k_v37_decoy.fasta
outputdir=${inputpath}/6Fusion_genefusion_unpair
genefuse -t 20 -r ${hg19} -f /cgdata/liuxiangqiong/software/GeneFuse-master/genes/cancer.b37.csv -1 ${inputpath}/${tumor}_clean_R1.fq.gz -2 ${inputpath}/${tumor}_clean_R2.fq.gz  -h ${outputdir}/${tumor}_report.html -j ${outputdir}/${tumor}_report.json> ${outputdir}/${tumor}_fusion_GeneFusion.txt
rm -rf  ${inputpath}/${tumor}_clean_R1.fq.gz
rm -rf ${inputpath}/${tumor}_clean_R2.fq.gz
#进行处理
#python3 /cgdata/liuxiangqiong/work62pancancer/Client/v0/script/20220705/datafile_fusion_v0_20220914_finish.py -i ${inputpath} -s ${tumor}
#python3 /cgdata/liuxiangqiong/work62pancancer/Client/v0/script/20220705/datafile_fusion_v0_20230228_finish.py -i ${inputpath} -s ${tumor}
python3 /cgdata/liuxiangqiong/work62pancancer/Client/v0/script/20220705/datafile_fusion_v0_20230403_finish.py -i ${inputpath} -s ${tumor}