From 04d7650bb4125b3754db1c6a487babc50c7d03b1 Mon Sep 17 00:00:00 2001
From: Brandi Cantarel <brandi.cantarel@utsouthwestern.edu>
Date: Thu, 30 Jul 2020 15:50:11 -0500
Subject: [PATCH] update bedtools genomecov to reduce memory usage
---
alignment/bamqc.sh | 5 +++--
1 file changed, 3 insertions(+), 2 deletions(-)
diff --git a/alignment/bamqc.sh b/alignment/bamqc.sh
index 1496dad..acd91a8 100644
--- a/alignment/bamqc.sh
+++ b/alignment/bamqc.sh
@@ -79,7 +79,8 @@ fi
if [[ $nuctype == 'dna' ]]
then
- bedtools coverage -a ${bed} -b ${sbam} -hist > ${pair_id}.covhist.txt
+ bedtools sort -faidx $index_path/genome.fa.fai -i ${bed} > panel.sorted.bed
+ bedtools coverage -sorted -g ${index_path}/genomefile.txt -a panel.sorted.bed -b ${sbam} -hist > ${pair_id}.covhist.txt
grep ^all ${pair_id}.covhist.txt > ${pair_id}.genomecov.txt
perl $baseDir/calculate_depthcov.pl ${pair_id}.covhist.txt
if [[ -z $skiplc ]]
@@ -87,8 +88,8 @@ then
samtools view -@ $threads -b -L ${bed} -o ${pair_id}.ontarget.bam ${sbam}
samtools index -@ $threads ${pair_id}.ontarget.bam
samtools flagstat ${pair_id}.ontarget.bam > ${pair_id}.ontarget.flagstat.txt
- samtools view -@ $threads -b -q 1 ${sbam} | bedtools coverage -hist -b stdin -a ${bed} > ${pair_id}.mapqualcov.txt
java -Xmx64g -Djava.io.tmpdir=${tmpdir} -XX:ParallelGCThreads=$threads -jar $PICARD/picard.jar EstimateLibraryComplexity BARCODE_TAG=RG I=${sbam} OUTPUT=${pair_id}.libcomplex.txt TMP_DIR=${tmpdir}
+ #samtools view -@ $threads -b -q 1 ${sbam} | bedtools coverage -hist -b stdin -a ${bed} > ${pair_id}.mapqualcov.txt
#java -Xmx64g -Djava.io.tmpdir=${tmpdir} -jar $PICARD/picard.jar CollectAlignmentSummaryMetrics R=${index_path}/genome.fa I=${pair_id}.ontarget.bam OUTPUT=${pair_id}.alignmentsummarymetrics.txt TMP_DIR=${tmpdir}
#samtools view -@ $threads ${sbam} | awk '{sum+=$5} END { print "Mean MAPQ =",sum/NR}' > ${pair_id}.meanmap.txt
fi
--
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