updates pipeline

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 scatter ${pair_id}.cnr -s ${pair_id}.call.cns -o ${pair_id}.cnv.scatter.pdf
+cnvkit.py scatter ${pair_id}.cnr -s ${pair_id}.call.cns -t --segment-color "blue" -o ${pair_id}.cnv.scatter.pdf
 perl $baseDir/filter_cnvkit.pl *.call.cns

variants/unionvcf.pl

@@ -97,7 +97,7 @@ foreach $vcf (@vcffiles) {
       }
       my $mafs = '.';
       my @maf = ();
-      if ($gtdata{DP} && $gtdata{DP} ne '.' && $gtdata{AO} && $gtdata{AO} ne '.') {
+      if ($gtdata{DP} && $gtdata{DP} ne '.' && exists $gtdata{AO} && $gtdata{AO} ne '.') {
 	foreach $areadct (split(/,/,$gtdata{AO})) {
 	  push @maf, sprintf("%.2f",$areadct/$gtdata{DP});
 	}