- #!/bin/sh
- #PBS -N Genefusion
- #PBS -j oe
- #PBS -l ncpus=12
- #PBS -l nodes=1
- #PBS -l mem=20G
- #inputpath=$1
- #sample=$2
- source /home/liuxiangqiong/miniconda3/bin/activate base
- hg19=/cgdata/Database/GATK/b37/human_g1k_v37_decoy.fasta
- outputdir=${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
|
