multithreaded bamqc

alignment/bamqc.sh

@@ -44,15 +44,15 @@ fi
 
 if [[ $nuctype == 'dna' ]]; then
     module load bedtools/2.26.0 picard/2.10.3
-    samtools view -b --threads $SLURM_CPUS_ON_NODE -L ${bed} -o ${pair_id}.ontarget.bam ${sbam}
-    samtools index ${pair_id}.ontarget.bam
+    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 $PICARD/picard.jar CollectInsertSizeMetrics INPUT=${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 -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 -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 ${sbam} | awk '{sum+=$5} END { print "Mean MAPQ =",sum/NR}' > ${pair_id}.meanmap.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

alignment/starfusion.sh

@@ -33,7 +33,7 @@ fi
 index_path=${refgeno}/CTAT_lib/
 baseDir="`dirname \"$0\"`"
 source /etc/profile.d/modules.sh
-module add python/2.7.x-anaconda star/2.5.2b
+module add python/2.7.x-anaconda star/2.5.2b bedtools/2.26.0
 STAR-Fusion --genome_lib_dir ${index_path} --left_fq ${fq1} --right_fq ${fq2} --output_dir star_fusion &> star_fusion.err
 mv star_fusion/star-fusion.fusion_candidates.final.abridged ${pair_id}.starfusion.txt