#!/bin/sh
#PBS -N noUMI_unpair
#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
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
#$cmddir/s5_noUMI_Germline_gatk_unpair_20220921.sh
#$cmddir/s5_noUMI_Germline_gatk_unpair_20220929.sh
$cmddir/s5_noUMI_Germline_gatk_unpair_20230522.sh

#for chemical
echo "for HL sites"
#$cmddir/s6_noUMI_HL_gatk_unpair_20220606.sh
$cmddir/s6_noUMI_HL_gatk_unpair_20220929.sh
#for HLA
echo "for HLA"
#$cmddir/s8_noUMI_HLA_hlahd_unpair_20220606.pbs
$cmddir/s8_noUMI_HLA_hlahd_unpair_20220929.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