prod_reproduction/202307-FeBY2/run_qc.pbs

#!/bin/sh
#PBS -N qc
#PBS -j oe
#PBS -l ncpus=4
#PBS -l nodes=1
#PBS -l mem=20G
cd ${PBS_O_WORKDIR}
set -e 

. $feby2_script/conf/feby2.cfg
test -d conest || mkdir conest
bia_snp=$bia_snp
echo $panel
echo $target
echo $bia_snp
## Contamination chech
$verify --vcf $bia_snp --bam $bam_dir/${sample}.bam --out conest/${sample}.verify --verbose --ignoreRG &
$gatk4 GetPileupSummaries -I $bam_dir/${sample}.bam -L $target -V $bia_snp -max-af 0.99 -min-af 0.01 -O conest/${sample}.ps.tab
$gatk4 CalculateContamination -I conest/${sample}.ps.tab -O conest/${sample}.contEST.tab

## Picard
test -d picard || mkdir picard
$gatk4 CollectHsMetrics -I $bam_dir/${sample}.bam -BI $interval -TI $interval -O picard/${sample}_hs_metrics.txt -R $ref --COVERAGE_CAP 6000 -MQ 0 --CLIP_OVERLAPPING_READS false &

test -d log || mkdir log
wait
touch log/$sample.finished