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- #!/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
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