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- outdir=$1
- readsID=$2
- sortedBam=$3
- curPath=$(dirname $(readlink -f "$0"))
- subPath=$(dirname $(readlink -f $curPath))
- target_gene_gtf=${subPath}/DB/target_gene_gtf.txt
- blacklist_file=${subPath}/DB/FusionBlackList.txt
- fusion_parterner=${subPath}/DB/fusion_gene_parterner_exonID.txt
- homo_file=${subPath}/DB/primer_home_stat.txt
- info_file=${subPath}/DB/primer_info_final.txt
- python $subPath/py_script/breakpoint_search_v6.3.py -i $sortedBam -o $outdir;
- python $subPath/py_script/breakpoint_stat_v6.3.py -i $outdir -r $readsID;
- python $subPath/py_script/breakpoint_stat_single_v6.3.py -i $outdir -r $readsID -m $homo_file -f $info_file;
- python $subPath/py_script/breakpoint_anno_v6.3.py -i $outdir/fusion_stat_final.txt -t $target_gene_gtf -o $outdir/fusion_stat_final_anno.txt;
- python $subPath/py_script/breakpoint_anno_single_v6.3.py -i $outdir/single_stat.txt -t $target_gene_gtf -o $outdir/single_stat_anno.txt;
- python $subPath/py_script/breakpoint_filter_v6.3.py -i $outdir -b $blacklist_file -t $fusion_parterner
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