From 1fa984adda0478775c50913cdf35b2f65720350f Mon Sep 17 00:00:00 2001
From: Brandi Cantarel <brandi.cantarel@utsouthwestern.edu>
Date: Mon, 6 Nov 2017 16:41:36 -0600
Subject: [PATCH] prepare_release
---
alignment/starfusion.sh | 2 +-
variants/gatkrunner.sh | 2 +-
2 files changed, 2 insertions(+), 2 deletions(-)
diff --git a/alignment/starfusion.sh b/alignment/starfusion.sh
index cad5ba9..842894c 100644
--- a/alignment/starfusion.sh
+++ b/alignment/starfusion.sh
@@ -7,7 +7,7 @@ usage() {
echo "-a --FastQ R1"
echo "-b --FastQ R2"
echo "-p --Prefix for output file name"
- echo "Example: bash hisat.sh -p prefix -r GRCh38 -a SRR1551047_1.fastq.gz -b SRR1551047_2.fastq.gz"
+ echo "Example: bash starfusion.sh -p prefix -r /project/shared/bicf_workflow_ref/GRCh38 -a SRR1551047_1.fastq.gz -b SRR1551047_2.fastq.gz"
exit 1
}
OPTIND=1 # Reset OPTIND
diff --git a/variants/gatkrunner.sh b/variants/gatkrunner.sh
index 7918eca..bcf723d 100644
--- a/variants/gatkrunner.sh
+++ b/variants/gatkrunner.sh
@@ -66,7 +66,7 @@ then
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 $GATK_JAR -T SplitNCigarReads -R ${reffa} -I ${pair_id}.clean.bam -o ${pair_id}.split.bam -rf ReassignOneMappingQuality -RMQF 255 -RMQT 60 -U ALLOW_N_CIGAR_READS
+ 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
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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