update svcalling for merging sv and create bed

variants/svcalling.sh

@@ -104,15 +104,14 @@ then
 	svaba run -p $NPROC -G ${reffa} -t ${sbam} -a ${pair_id}
     fi
     #Create SV FILE
-    bgzip -f ${pair_id}.svaba.unfiltered.sv.vcf
+    vcf-concat ${pair_id}.svaba.unfiltered*sv.vcf | perl -pe 's/\.consensus|\.bam//g' | vcf-sort| bgzip > ${pair_id}.svaba.unfiltered.sv.vcf.gz
     bash $baseDir/norm_annot.sh -r ${index_path} -p svaba.sv -v ${pair_id}.svaba.unfiltered.sv.vcf.gz
-    java -Xmx10g -jar $SNPEFF_HOME/snpEff.jar -no-intergenic -lof -c $SNPEFF_HOME/snpEff.config ${snpeffgeno} svaba.sv.norm.vcf.gz | java -jar $SNPEFF_HOME/SnpSift.jar filter "( GEN[*].DP >= 20)" | bgzip > ${pair_id}.svaba.sv.vcf.gz
+    java -Xmx10g -jar $SNPEFF_HOME/snpEff.jar -no-intergenic -lof -c $SNPEFF_HOME/snpEff.config ${snpeffgeno} svaba.sv.norm.vcf.gz | java -jar $SNPEFF_HOME/SnpSift.jar filter "( GEN[*].AD >= 20)" | bgzip > ${pair_id}.svaba.sv.vcf.gz
 
-    java -jar $SNPEFF_HOME/SnpSift.jar filter "( SPAN >= 20)" ${pair_id}.svaba.unfiltered.indel.vcf |bgzip > ${pair_id}.svaba.indel.vcf.gz
+    vcf-concat ${pair_id}.svaba.unfiltered*indel.vcf | perl -pe 's/\.consensus|\.bam//g' | vcf-sort | java -jar $SNPEFF_HOME/SnpSift.jar filter "( SPAN >= 20)" - |bgzip > ${pair_id}.svaba.indel.vcf.gz
     bash $baseDir/norm_annot.sh -r ${index_path} -p svaba.indel -v ${pair_id}.svaba.indel.vcf.gz
     java -Xmx10g -jar $SNPEFF_HOME/snpEff.jar -no-intergenic -lof -c $SNPEFF_HOME/snpEff.config ${snpeffgeno} svaba.indel.norm.vcf.gz | bgzip > ${pair_id}.svaba.vcf.gz
 
-
     if [[ $filter == 1 ]]
     then
 	zgrep '#CHROM' ${pair_id}.svaba.sv.vcf.gz > ${pair_id}.svaba.genefusion.txt

variants/uniform_vcf_gt.pl

@@ -58,12 +58,15 @@ while (my $line = <VCF>) {
 	  foreach (@alts) {
 	      $gtdata{DP} += $_;
 	  }
+      } elsif ($gtdata{AD} =~ m/^\d+$/){
+	  $gtdata{AO} = $gtdata{AD};
+	  $gtdata{RO} = $gtdata{DP} - $gtdata{AO};
+	  $gtdata{AD} = join(',',$gtdata{RO},$gtdata{AO});
       } elsif (exists $gtdata{DV} && exists $gtdata{RV}) {
 	  $gtdata{AO} = $gtdata{DV} + $gtdata{RV};
 	  $gtdata{RO} = $gtdata{DR} + $gtdata{RR};
 	  $gtdata{AD} = join(',',$gtdata{RO},$gtdata{AO});
 	  $gtdata{DP} = $gtdata{RO}+$gtdata{AO};
-	  
       } elsif (exists $gtdata{DR} && exists $gtdata{SR}){
 	  $gtdata{AO} = $gtdata{AD};
 	  $gtdata{DP} = $gtdata{AO} unless $gtdata{DP};