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- #!/bin/sh
- #PBS -N noUMI_SNVpair
- #PBS -j oe
- #PBS -l ncpus=20
- #PBS -l nodes=1
- #PBS -l mem=40G
- source /home/liuxiangqiong/miniconda3/bin/activate base
- cmddir=/cgdata/liuxiangqiong/work62pancancer/Client/v0/script/20220705
- #for sv calling
- #for sv calling with varscan
- starttime="`date '+%Y%m%d%H%M%S'`"
- 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
- $cmddir/s2_noUMI_sv_calling_vardict_pair_20221027.pbs &
- echo "for sv calling pair with varscan"
- #$cmddir/s2_noUMI_sv_calling_varscan_pair_20220705.pbs
- #$cmddir/s2_noUMI_sv_calling_varscan_pair_20220901.pbs
- #$cmddir/s2_noUMI_sv_calling_varscan_pair_20220929.pbs
- #$cmddir/s2_noUMI_sv_calling_varscan_pair_20221027.pbs &
- #$cmddir/s2_noUMI_sv_calling_varscan_pair_20221226.pbs &
- $cmddir/s2_noUMI_sv_calling_varscan_pair_20230209.pbs &
- wait
- ##对varscan和vardict的方法结合获得最后的突变
- python3 /cgdata/liuxiangqiong/work62pancancer/Client/v0/script/20220705/datafile_somatic_filter_mergeresult_v0_20230331_finish.py -i ${inputpath} -s ${sample}
- #for CNV paired
- #echo "for CNV pair with cnvkit"
- #$cmddir/s3_noUMI_CNV_cnvkit_pair_20220606.sh
- #$cmddir/s3_noUMI_CNV_cnvkit_pair_20220929.sh
- #for MSI paired
- #echo "for MSI pair"
- #$cmddir/s4_noUMI_MSI_15STR_msisensor2_pair_20220606.sh
- #$cmddir/s4_noUMI_MSI_15STR_msisensor2_pair_20220929.sh
- #for fusion Manta paired
- #echo "for fusion Manta pair"
- #$cmddir/s7_noUMI_fusion_manta_pair_20220606.sh
- ###for igv report
- $cmddir/s12_igv_report_pair_20230210.sh
- ##for sample pair concordance
- $cmddir/s13_sample_concordance_pair_20230210.sh
- endtime="`date '+%Y%m%d%H%M%S'`"
- echo "run " $[$endtime-$starttime]"s">${inputpath}/${sample}_sv_pair.log1
- echo "${sample} pair of somatic finish!" >>${inputpath}/${sample}_sv_pair.log1
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