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- #!/bin/sh
- #PBS -N noUMI_unpair
- #PBS -j oe
- #PBS -l ncpus=20
- #PBS -l nodes=1
- #PBS -l mem=30G
- source /home/liuxiangqiong/miniconda3/bin/activate base
- cmddir=/cgdata/liuxiangqiong/work62pancancer/Client/v0/script/20220606
- starttime="`date '+%Y%m%d%H%M%S'`"
- echo "for germline"
- #$cmddir/s5_noUMI_Germline_gatk_unpair_20220606.sh
- #$cmddir/s5_noUMI_Germline_gatk_unpair_20220824.sh
- $cmddir/s5_noUMI_Germline_gatk_unpair_20220921.sh
- #for chemical
- echo "for HL sites"
- $cmddir/s6_noUMI_HL_gatk_unpair_20220606.sh
- #for HLA
- echo "for HLA"
- $cmddir/s8_noUMI_HLA_hlahd_unpair_20220606.pbs
- endtime="`date '+%Y%m%d%H%M%S'`"
- echo "run " $[$endtime-$starttime]"s">${inputpath}/${sample}_germHLAHL_unpair.log1
- echo "${sample} germline,HL and HLA finish!" >>${inputpath}/${sample}_germHLAHL_unpair.log1
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