#!/bin/sh
#PBS -N noUMI_pair
#PBS -j oe
#PBS -l ncpus=20
#PBS -l nodes=1
#PBS -l mem=50G
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
$cmddir/s2_noUMI_sv_calling_vardict_pair_20220929.pbs
echo "for sv calling pair with varscan"
#$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
$cmddir/s2_noUMI_sv_calling_varscan_pair_20221025.pbs
#for CNV paired
echo "for CNV pair with cnvkit"
#$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
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