From 6dd512060a05bb78002090ebbe7bebf15317bc3e Mon Sep 17 00:00:00 2001
From: Brandi Cantarel <brandi.cantarel@utsouthwestern.edu>
Date: Wed, 14 Feb 2018 14:19:22 -0600
Subject: [PATCH] update gatkrunner
---
variants/gatkrunner.sh | 5 +++--
1 file changed, 3 insertions(+), 2 deletions(-)
diff --git a/variants/gatkrunner.sh b/variants/gatkrunner.sh
index e90ad2e..743f576 100644
--- a/variants/gatkrunner.sh
+++ b/variants/gatkrunner.sh
@@ -65,8 +65,8 @@ then
module load picard/2.10.3
java -Xmx4g -jar $PICARD/picard.jar CleanSam INPUT=${sbam} OUTPUT=${pair_id}.clean.bam
java -Xmx4g -jar $PICARD/picard.jar ReorderSam I=${pair_id}.clean.bam O=${pair_id}.sort.bam R=${reffa} CREATE_INDEX=TRUE
- #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
+ 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
java -Xmx4g -jar $GATK_JAR -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 -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 -I ${pair_id}.split.bam -R ${reffa} --filter_mismatching_base_and_quals -T IndelRealigner -targetIntervals ${pair_id}.bam.list -o ${pair_id}.realigned.bam
@@ -74,6 +74,7 @@ then
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
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 $SLURM_CPUS_ON_NODE -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 $SLURM_CPUS_ON_NODE
--
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