From 8140bbee9d05fa3553cbca141db1fb968f05be6d Mon Sep 17 00:00:00 2001
From: Brandi Cantarel <brandi.cantarel@utsouthwestern.edu>
Date: Thu, 20 Sep 2018 16:13:28 -0500
Subject: [PATCH] memory 16GB for GATK
---
variants/gatkrunner.sh | 12 ++++++------
1 file changed, 6 insertions(+), 6 deletions(-)
diff --git a/variants/gatkrunner.sh b/variants/gatkrunner.sh
index 864331c..4a610ad 100755
--- a/variants/gatkrunner.sh
+++ b/variants/gatkrunner.sh
@@ -69,14 +69,14 @@ then
samtools index -@ $SLURM_CPUS_ON_NODE ${pair_id}.clean.bam
java -Xmx4g -jar $GATK_JAR -L ${index_path}/../gatk_regions.list -T SplitNCigarReads -R ${reffa} -I ${pair_id}.sort.bam -o ${pair_id}.split.bam -rf ReassignOneMappingQuality -RMQF 255 -RMQT 60 -U ALLOW_N_CIGAR_READS
java -Xmx32g -jar $GATK_JAR -L ${index_path}/../gatk_regions.list -T RealignerTargetCreator -known ${knownindel} -R ${reffa} -o ${pair_id}.bam.list -I ${pair_id}.split.bam -nt 8 -nct 1
- java -Xmx32g -jar $GATK_JAR -L ${index_path}/../gatk_regions.list -I ${pair_id}.split.bam -R ${reffa} --filter_mismatching_base_and_quals -T IndelRealigner -targetIntervals ${pair_id}.bam.list -o ${pair_id}.realigned.bam
- java -Xmx32g -jar $GATK_JAR -l INFO -R ${reffa} --knownSites ${dbsnp} -I ${pair_id}.realigned.bam -T BaseRecalibrator -cov ReadGroupCovariate -cov QualityScoreCovariate -cov CycleCovariate -cov ContextCovariate -o ${pair_id}.recal_data.grp -nt 1 -nct 8
- java -Xmx32g -jar $GATK_JAR -L ${index_path}/../gatk_regions.list -T PrintReads -R ${reffa} -I ${pair_id}.realigned.bam -BQSR ${pair_id}.recal_data.grp -o ${pair_id}.final.bam -nt 1 -nct 8
+ java -Xmx16g -jar $GATK_JAR -L ${index_path}/../gatk_regions.list -I ${pair_id}.split.bam -R ${reffa} --filter_mismatching_base_and_quals -T IndelRealigner -targetIntervals ${pair_id}.bam.list -o ${pair_id}.realigned.bam
+ java -Xmx16g -jar $GATK_JAR -l INFO -R ${reffa} --knownSites ${dbsnp} -I ${pair_id}.realigned.bam -T BaseRecalibrator -cov ReadGroupCovariate -cov QualityScoreCovariate -cov CycleCovariate -cov ContextCovariate -o ${pair_id}.recal_data.grp -nt 1 -nct 8
+ java -Xmx16g -jar $GATK_JAR -L ${index_path}/../gatk_regions.list -T PrintReads -R ${reffa} -I ${pair_id}.realigned.bam -BQSR ${pair_id}.recal_data.grp -o ${pair_id}.final.bam -nt 1 -nct 8
elif [[ $algo == 'gatkbam' ]]
then
samtools index -@ $SLURM_CPUS_ON_NODE ${sbam}
- java -Xmx32g -jar $GATK_JAR -T RealignerTargetCreator -known ${knownindel} -R ${reffa} -o ${pair_id}.bam.list -I ${sbam} -nt 8 -nct 1
- java -Xmx32g -jar $GATK_JAR -I ${sbam} -R ${reffa} --filter_mismatching_base_and_quals -T IndelRealigner -targetIntervals ${pair_id}.bam.list -o ${pair_id}.realigned.bam
- java -Xmx32g -jar $GATK_JAR -l INFO -R ${reffa} --knownSites ${dbsnp} -I ${pair_id}.realigned.bam -T BaseRecalibrator -cov ReadGroupCovariate -cov QualityScoreCovariate -cov CycleCovariate -cov ContextCovariate -o ${pair_id}.recal_data.grp -nt 1 -nct 8
+ java -Xmx16g -jar $GATK_JAR -T RealignerTargetCreator -known ${knownindel} -R ${reffa} -o ${pair_id}.bam.list -I ${sbam} -nt 8 -nct 1
+ java -Xmx16g -jar $GATK_JAR -I ${sbam} -R ${reffa} --filter_mismatching_base_and_quals -T IndelRealigner -targetIntervals ${pair_id}.bam.list -o ${pair_id}.realigned.bam
+ java -Xmx16g -jar $GATK_JAR -l INFO -R ${reffa} --knownSites ${dbsnp} -I ${pair_id}.realigned.bam -T BaseRecalibrator -cov ReadGroupCovariate -cov QualityScoreCovariate -cov CycleCovariate -cov ContextCovariate -o ${pair_id}.recal_data.grp -nt 1 -nct 8
java -Xmx16g -jar $GATK_JAR -T PrintReads -R ${reffa} -I ${pair_id}.realigned.bam -BQSR ${pair_id}.recal_data.grp -o ${pair_id}.final.bam -nt 1 -nct 8
fi
--
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