From 283e3ecd3626d7a0d379d6e884942d32e61f4ae3 Mon Sep 17 00:00:00 2001
From: Brandi Cantarel <brandi.cantarel@utsouthwestern.edu>
Date: Mon, 8 Jul 2019 17:20:09 -0500
Subject: [PATCH] add skip to qc steps when not necessary
---
alignment/bamqc.sh | 20 ++++++++++++--------
1 file changed, 12 insertions(+), 8 deletions(-)
diff --git a/alignment/bamqc.sh b/alignment/bamqc.sh
index 91ddb95..18dbb9e 100644
--- a/alignment/bamqc.sh
+++ b/alignment/bamqc.sh
@@ -13,7 +13,7 @@ usage() {
exit 1
}
OPTIND=1 # Reset OPTIND
-while getopts :r:b:c:n:p:d:h opt
+while getopts :r:b:c:n:p:s:d:h opt
do
case $opt in
r) index_path=$OPTARG;;
@@ -22,6 +22,7 @@ do
n) nuctype=$OPTARG;;
p) pair_id=$OPTARG;;
d) dedup=$OPTARG;;
+ s) skiplc=1;
h) usage;;
esac
done
@@ -52,15 +53,18 @@ fi
if [[ $nuctype == 'dna' ]]; then
module load bedtools/2.26.0 picard/2.10.3
- samtools view -@ $SLURM_CPUS_ON_NODE -b -L ${bed} -o ${pair_id}.ontarget.bam ${sbam}
- samtools index -@ $SLURM_CPUS_ON_NODE ${pair_id}.ontarget.bam
- samtools flagstat ${pair_id}.ontarget.bam > ${pair_id}.ontarget.flagstat.txt
+ if [[ -z $skiplc ]]
+ then
+ samtools view -@ $SLURM_CPUS_ON_NODE -b -L ${bed} -o ${pair_id}.ontarget.bam ${sbam}
+ samtools index -@ $SLURM_CPUS_ON_NODE ${pair_id}.ontarget.bam
+ samtools flagstat ${pair_id}.ontarget.bam > ${pair_id}.ontarget.flagstat.txt
+ java -Xmx64g -jar $PICARD/picard.jar CollectAlignmentSummaryMetrics R=${index_path}/genome.fa I=${pair_id}.ontarget.bam OUTPUT=${pair_id}.alignmentsummarymetrics.txt
+ java -Xmx64g -XX:ParallelGCThreads=$SLURM_CPUS_ON_NODE -jar $PICARD/picard.jar EstimateLibraryComplexity I=${sbam} OUTPUT=${pair_id}.libcomplex.txt
+ samtools view -@ $SLURM_CPUS_ON_NODE -b -q 1 ${sbam} | bedtools coverage -sorted -hist -g ${index_path}/genomefile.txt -b stdin -a ${bed} > ${pair_id}.mapqualcov.txt
+ samtools view -@ $SLURM_CPUS_ON_NODE ${sbam} | awk '{sum+=$5} END { print "Mean MAPQ =",sum/NR}' > ${pair_id}.meanmap.txt
+ fi
java -Xmx64g -jar $PICARD/picard.jar CollectInsertSizeMetrics INPUT=${sbam} HISTOGRAM_FILE=${pair_id}.hist.ps REFERENCE_SEQUENCE=${index_path}/genome.fa OUTPUT=${pair_id}.hist.txt
- java -Xmx64g -jar $PICARD/picard.jar CollectAlignmentSummaryMetrics R=${index_path}/genome.fa I=${pair_id}.ontarget.bam OUTPUT=${pair_id}.alignmentsummarymetrics.txt
- java -Xmx64g -jar $PICARD/picard.jar EstimateLibraryComplexity I=${sbam} OUTPUT=${pair_id}.libcomplex.txt
- samtools view -@ $SLURM_CPUS_ON_NODE -b -q 1 ${sbam} | bedtools coverage -sorted -hist -g ${index_path}/genomefile.txt -b stdin -a ${bed} > ${pair_id}.mapqualcov.txt
bedtools coverage -sorted -g ${index_path}/genomefile.txt -a ${bed} -b ${sbam} -hist > ${pair_id}.covhist.txt
grep ^all ${pair_id}.covhist.txt > ${pair_id}.genomecov.txt
- samtools view -@ $SLURM_CPUS_ON_NODE ${sbam} | awk '{sum+=$5} END { print "Mean MAPQ =",sum/NR}' > ${pair_id}.meanmap.txt
perl $baseDir/calculate_depthcov.pl ${pair_id}.covhist.txt
fi
--
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