180720 errors

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