update pindel for comparison w/ itdseeker

variants/itdseek.sh

@@ -50,6 +50,7 @@ source /etc/profile.d/modules.sh
 module load samtools/gcc/1.8 snpeff/4.3q vcftools/0.1.14 htslib/gcc/1.8 bcftools/gcc/1.8 bedtools/2.26.0 
 stexe=`which samtools`
 
-samtools view -@ $SLURM_CPUS_ON_NODE -L ${itdbed} ${sbam} | /project/shared/bicf_workflow_ref/seqprg/itdseek-1.2/itdseek.pl --refseq ${reffa} --samtools ${stexe} --bam ${sbam} | vcf-sort |bgzip > ${pair_id}.itdseek.vcf.gz
+samtools view -@ $SLURM_CPUS_ON_NODE -L ${itdbed} ${sbam} | /project/shared/bicf_workflow_ref/seqprg/itdseek-1.2/itdseek.pl --refseq ${reffa} --samtools ${stexe} --bam ${sbam} | vcf-sort | bedtools intersect -header -b ${itdbed} -a stdin | bgzip > ${pair_id}.itdseek.vcf.gz
 tabix ${pair_id}.itdseek.vcf.gz
-bcftools norm --fasta-ref $reffa -m - -Oz ${pair_id}.itdseek.vcf.gz | bedtools intersect -header -b ${itdbed} -a stdin | java -Xmx10g -jar $SNPEFF_HOME/snpEff.jar -no-intergenic -lof -c $SNPEFF_HOME/snpEff.config GRCh38.86 - |bgzip > ${pair_id}.itdseek_tandemdup.vcf.gz
+bcftools norm --fasta-ref $reffa -m - -Oz ${pair_id}.itdseek.vcf.gz | java -Xmx10g -jar $SNPEFF_HOME/snpEff.jar -no-intergenic -lof -c $SNPEFF_HOME/snpEff.config GRCh38.86 - |bgzip > ${pair_id}.itdseek_tandemdup.vcf.gz
+ 

variants/parse_pindel.pl

@@ -75,16 +75,14 @@ while (my $line = <VCF>) {
     push @newgts, join(":",$gtdata{GT},$gtdata{DP},$gtdata{AD},$gtdata{AO},$gtdata{RO});
   }
   next if ($missingGT == scalar(@gts));
-
+  
   if ($hash{SVTYPE} eq 'DUP:TANDEM') {
-    print DUP join("\t",$chrom,$pos,$id,'N','<DUP>',$score,$filter,$annot,$newformat,@newgts),"\n";
-  }elsif ($hash{SVTYPE} eq 'INS') {
-    print SV join("\t",$chrom,$pos,$id,'N','<INS>',$score,$filter,$annot,$newformat,@newgts),"\n";
+    print DUP join("\t",$chrom,$pos,$id,$ref,$alt,$score,$filter,$annot,$newformat,@newgts),"\n";
   }elsif ($hash{SVTYPE} eq 'DEL' || $hash{SVTYPE} eq 'INS') {
     if (abs($hash{SVLEN}) < 50) {
       print SI join("\t",$chrom,$pos,$id,$ref,$alt,$score,$filter,$annot,$newformat,@newgts),"\n";
     }else {
-	$newalt = "<".$hash{SVTYPE}.">";
+      $newalt = "<".$hash{SVTYPE}.">";
       print SV join("\t",$chrom,$pos,$id,'N',$newalt,$score,$filter,$annot,$newformat,@newgts),"\n";
     }
   }