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Commit 2df6acfa authored by Brandi Cantarel's avatar Brandi Cantarel
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gatk core dump fix

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variants/gatkrunner.sh
+ 6
− 7
View file @ 2df6acfa
...@@ -68,16 +68,15 @@ then ...@@ -68,16 +68,15 @@ then
java -Xmx4g -jar $PICARD/picard.jar AddOrReplaceReadGroups INPUT=${pair_id}.clean.bam O=${pair_id}.rg_added_sorted.bam SO=coordinate RGID=${pair_id} RGLB=tx RGPL=illumina RGPU=barcode RGSM=${pair_id} java -Xmx4g -jar $PICARD/picard.jar AddOrReplaceReadGroups INPUT=${pair_id}.clean.bam O=${pair_id}.rg_added_sorted.bam SO=coordinate RGID=${pair_id} RGLB=tx RGPL=illumina RGPU=barcode RGSM=${pair_id}
samtools index -@ $SLURM_CPUS_ON_NODE ${pair_id}.clean.bam 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 -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 $SLURM_CPUS_ON_NODE -nct 1 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 ${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 $SLURM_CPUS_ON_NODE 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 $SLURM_CPUS_ON_NODE 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
elif [[ $algo == 'gatkbam' ]] elif [[ $algo == 'gatkbam' ]]
then then
samtools index -@ $SLURM_CPUS_ON_NODE ${sbam} 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 $SLURM_CPUS_ON_NODE -nct 1 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 -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 $SLURM_CPUS_ON_NODE 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 -T PrintReads -R ${reffa} -I ${pair_id}.realigned.bam -BQSR ${pair_id}.recal_data.grp -o ${pair_id}.final.bam -nt 1 -nct $SLURM_CPUS_ON_NODE 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 fi
variants/somatic_vc.sh
+ 1
− 1
View file @ 2df6acfa
...@@ -129,7 +129,7 @@ then ...@@ -129,7 +129,7 @@ then
module rm java/oracle/jdk1.7.0_51 module rm java/oracle/jdk1.7.0_51
module load snpeff/4.3q module load snpeff/4.3q
samtools mpileup -C 50 -f ${reffa} $tumor > t.mpileup samtools mpileup -C 50 -f ${reffa} $tumor > t.mpileup
samtools mpileup -C 50 -f ${reffa} $normal > t.mpileup samtools mpileup -C 50 -f ${reffa} $normal > n.mpileup
VarScan somatic n.mpileup t.mpileup vscan --output-vcf 1 VarScan somatic n.mpileup t.mpileup vscan --output-vcf 1
VarScan copynumber n.mpileup t.mpileup vscancnv VarScan copynumber n.mpileup t.mpileup vscancnv
vcf-concat vscan*.vcf | vcf-sort | vcf-annotate -n --fill-type -n | java -jar $SNPEFF_HOME/SnpSift.jar filter '((exists SOMATIC) & (GEN[*].DP >= 10))' | perl -pe "s/TUMOR/${tid}/" | perl -pe "s/NORMAL/${nid}/g" | bgzip > ${pair_id}.varscan.vcf.gz vcf-concat vscan*.vcf | vcf-sort | vcf-annotate -n --fill-type -n | java -jar $SNPEFF_HOME/SnpSift.jar filter '((exists SOMATIC) & (GEN[*].DP >= 10))' | perl -pe "s/TUMOR/${tid}/" | perl -pe "s/NORMAL/${nid}/g" | bgzip > ${pair_id}.varscan.vcf.gz
......
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