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Commit 8140bbee authored by Brandi Cantarel's avatar Brandi Cantarel
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memory 16GB for GATK

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variants/gatkrunner.sh
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......@@ -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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