From bdc57626f002bb5ff7ce2e6d3e7f7682be0e4d50 Mon Sep 17 00:00:00 2001
From: Erika Villa <Erika.Villa@utsouthwestern.edu>
Date: Mon, 23 Jul 2018 11:52:14 -0500
Subject: [PATCH] 180720 errors
---
alignment/bamqc.sh | 1 +
1 file changed, 1 insertion(+)
diff --git a/alignment/bamqc.sh b/alignment/bamqc.sh
index 2e9f460..04de66d 100644
--- a/alignment/bamqc.sh
+++ b/alignment/bamqc.sh
@@ -47,6 +47,7 @@ if [[ $nuctype == 'dna' ]]; then
samtools view -b --threads $SLURM_CPUS_ON_NODE -L ${bed} -o ${pair_id}.ontarget.bam ${sbam}
samtools index ${pair_id}.ontarget.bam
samtools flagstat ${pair_id}.ontarget.bam > ${pair_id}.ontarget.flagstat.txt
+ samtools view -b -F 1024 ${pair_id}.ontarget.bam | bedtools coverage -sorted -g ${index_path}/genomefile.txt -a ${bed} -b stdin -hist | grep ^all > ${pair_id}.dedupcov.txt
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=${sbam} OUTPUT=${pair_id}.alignmentsummarymetrics.txt
java -Xmx64g -jar $PICARD/picard.jar EstimateLibraryComplexity I=${sbam} OUTPUT=${pair_id}.libcomplex.txt
--
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