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- #!/bin/sh
- #PBS -N noUMI_pair
- #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/20220705
- #for sv calling
- #for sv calling with varscan
- echo "for sv calling pair with varscan"
- starttime="`date '+%Y%m%d%H%M%S'`"
- #$cmddir/s2_noUMI_sv_calling_varscan_pair_20220705.pbs
- $cmddir/s2_noUMI_sv_calling_varscan_pair_20220901.pbs
- echo "for sv calling pair with vardict"
- #$cmddir/s2_noUMI_sv_calling_vardict_pair_20220615.pbs
- #$cmddir/s2_noUMI_sv_calling_vardict_pair_20220705.pbs
- $cmddir/s2_noUMI_sv_calling_vardict_pair_20220901.pbs
- #$cmddir/s2_noUMI_sv_calling_varscan_pair.pbs
- #for CNV paired
- echo "for CNV pair with cnvkit"
- $cmddir/s3_noUMI_CNV_cnvkit_pair_20220606.sh
- #for MSI paired
- echo "for MSI pair"
- $cmddir/s4_noUMI_MSI_15STR_msisensor2_pair_20220606.sh
- #for fusion Manta paired
- echo "for fusion Manta pair"
- $cmddir/s7_noUMI_fusion_manta_pair_20220606.sh
- endtime="`date '+%Y%m%d%H%M%S'`"
- echo "run " $[$endtime-$starttime]"s">${inputpath}/${sample}_svcnvMSI_pair.log1
- echo "${sample} pair of somatic CNV MSI finish!" >>${inputpath}/${sample}_svcnvMSI_pair.log1
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