#!/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