git fail friday

alignment/bamqc.sh

@@ -47,14 +47,12 @@ 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 -q 1 ${pair_id}.ontarget.bam | bedtools coverage -sorted -hist -g ${index_path}/genomefile.txt -b stdin -a ${bed}  >  ${pair_id}.mapqualcov.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 $PICARD/picard.jar CollectAlignmentSummaryMetrics R=${index_path}/genome.fa I=${pair_id}.ontarget.bam OUTPUT=${pair_id}.alignmentsummarymetrics.txt
-    java -Xmx64g -jar $PICARD/picard.jar EstimateLibraryComplexity I=${pair_id}.ontarget.bam OUTPUT=${pair_id}.libcomplex.txt
-    samtools view -F 1024 ${pair_id}.ontarget.bam | awk '{sum+=$5} END { print "Mean MAPQ =",sum/NR}' > ${pair_id}.meanmap.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
-    samtools view -b -q 1 ${pair_id}.ontarget.bam | bedtools coverage -sorted -hist -g ${index_path}/genomefile.txt -b stdin -a ${bed}  >  ${pair_id}.mapqualcov.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
+    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
-    perl $baseDir/calculate_depthcov.pl ${pair_id}.covhist.txt
     grep ^all ${pair_id}.covhist.txt >  ${pair_id}.genomecov.txt
+    samtools view ${pair_id}.dedup.bam | awk '{sum+=$5} END { print "Mean MAPQ =",sum/NR}' > ${pair_id}.meanmap.txt
+    perl $baseDir/calculate_depthcov.pl ${pair_id}.covhist.txt
  fi

variants/cnvkit.sh

@@ -61,5 +61,5 @@ cnvkit.py coverage ${sbam} ${targets}antitargets.bed -o ${pair_id}.antitargetcov
 cnvkit.py fix ${pair_id}.targetcoverage.cnn ${pair_id}.antitargetcoverage.cnn ${normals} -o ${pair_id}.cnr
 cnvkit.py segment ${pair_id}.cnr -o ${pair_id}.cns
 cnvkit.py call ${pair_id}.cns -o ${pair_id}.call.cns
-cnvkit.py diagram ${pair_id}.cnr -s ${pair_id}.cns -o ${pair_id}.cnv.pdf
+cnvkit.py scatter ${pair_id}.cnr -s ${pair_id}.call.cns -o ${pair_id}.cnv.scatter.pdf
 perl $baseDir/filter_cnvkit.pl *.call.cns

variants/unionvcf.pl

@@ -138,7 +138,7 @@ F1:foreach $chr (sort {$a cmp $b} keys %lines) {
 	my ($id,$dp,$maf) = split(/:/,$gtd);
 	push @{$csets{$id}}, [$caller,$dp,$maf];
       }
-      push @callset, join("/",$caller,$alt,@gtdesc);
+      push @callset, join("|",$caller,$alt,@gtdesc);
     }
     my $consistent = 1;
     foreach $id (keys %csets) {
@@ -152,7 +152,7 @@ F1:foreach $chr (sort {$a cmp $b} keys %lines) {
 	    $format,$gtsref,$gtdescref) = @{$lines{$chr}{$pos}{$caller}};
 	@gts = @{$gtsref};
 	@gtdesc = @{$gtdescref};
-	$annot = $annot.";CallSet=".join("|",@callset);
+	$annot = $annot.";CallSet=".join(",",@callset);
 	unless ($consistent) {
 	  $annot = $annot.";CallSetInconsistent=1";
 	}