add is docker to annot and update AD field for platypus

variants/annotvcf.sh

@@ -23,8 +23,11 @@ done
 
 shift $(($OPTIND -1))
 
-source /etc/profile.d/modules.sh
-module load bedtools/2.26.0  snpeff/4.3q
+if [[ -z $isdocker ]]
+then
+    source /etc/profile.d/modules.sh
+    module load bedtools/2.26.0  snpeff/4.3q
+fi
 
 if [[ $index_path == '/project/shared/bicf_workflow_ref/human/grch38_cloud/rnaref' ]]
 then

variants/uniform_vcf_gt.pl

@@ -93,6 +93,7 @@ while (my $line = <VCF>) {
 	  $gtdata{DP} = $gtdata{NR}; 	
 	  $gtdata{AO} = $gtdata{NV};
 	  $gtdata{RO} = $gtdata{DP} - $gtdata{AO};
+	  $gtdata{AD} = join(',',$gtdata{RO},$gtdata{AO});
       } elsif (exists $gtdata{AO} && exists $gtdata{RO}) {
 	  $gtdata{AD} = join(',',$gtdata{RO},$gtdata{AO});
 	  $gtdata{DP} = $gtdata{RO};