qc ontarget

alignment/bamqc.sh

@@ -46,9 +46,9 @@ 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 flagstat ${pair_id}.ontarget.bam > ${pair_id}.ontarget.flagstat.txt
+    #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=${sbam} OUTPUT=${pair_id}.alignmentsummarymetrics.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
     bedtools coverage -sorted -g  ${index_path}/genomefile.txt -a ${bed} -b ${sbam} -hist > ${pair_id}.covhist.txt

alignment/dnaseqalign.sh

@@ -50,12 +50,14 @@ else
     bwa mem -M -t $SLURM_CPUS_ON_NODE -R "@RG\tID:${pair_id}\tLB:tx\tPL:illumina\tPU:barcode\tSM:${pair_id}" ${index_path}/genome.fa ${fq1} > out.sam
 fi
 
-if [[ $umi == 'umi' ]]
+if [[ $umi == 'umi' ]] && [[ $index_path == '/project/shared/bicf_workflow_ref/GRCh38' ]]
 then
     k8 /cm/shared/apps/bwakit/0.7.15/bwa-postalt.js -p tmphla ${index_path}/genome.fa.alt out.sam | python ${baseDir}/add_umi_sam.py -s - -o output.unsort.bam
 elif [[ $index_path == '/project/shared/bicf_workflow_ref/GRCh38' ]]
 then
     k8 /cm/shared/apps/bwakit/0.7.15/bwa-postalt.js -p tmphla ${index_path}/genome.fa.alt out.sam| samtools view -1 - > output.unsort.bam
+elif [[ $umi == 'umi' ]] 
+    python ${baseDir}/add_umi_sam.py -s out.sam -o output.unsort.bam
 else 
     samtools view -1 -o output.unsort.bam out.sam
 fi