diff --git a/R/snv_merge_and_vaf_calc.R b/R/snv_merge_and_vaf_calc.R
index cf961c8..654da64 100755
--- a/R/snv_merge_and_vaf_calc.R
+++ b/R/snv_merge_and_vaf_calc.R
@@ -86,6 +86,7 @@ if (length(grep("\\.gz", muts_vcf)) > 0) {
 } else {
   num_snvs = system(paste("grep -cv \"^#\" ", muts_vcf, "|| true"), intern = TRUE)
 }
+num_snvs = as.integer(num_snvs)
 
 num_indels = 0
 if (indel_vcf != '-') {
@@ -96,6 +97,7 @@ if (indel_vcf != '-') {
     num_indels = system(paste("grep -cv \"^#\" ", indel_vcf, "|| true"), intern = TRUE)
   }
 }
+num_indels = as.integer(num_indels)
 
 col_t = c("character","numeric","character","character","character","character","character")
 if (num_snvs == 0) {
@@ -245,8 +247,8 @@ if (num_snvs > 0) {
       snvs_new2[new_row, "BEND"] = paste(snvs_tmp[, "BEND"], collapse = ",")
       snvs_new2[new_row, "TRI"] = snvs_tmp[1, "TRI"]
       snvs_new2[new_row, "QPOS"] = paste(snvs_tmp[, "QPOS"], collapse = ",")
-      snvs_new2[new_row, "DEPTH_FWD"] = median(snvs_tmp[, "DEPTH_FWD"])
-      snvs_new2[new_row, "DEPTH_REV"] = median(snvs_tmp[, "DEPTH_REV"])
+      snvs_new2[new_row, "DEPTH_FWD"] = median(as.numeric(snvs_tmp[, "DEPTH_FWD"]))
+      snvs_new2[new_row, "DEPTH_REV"] = median(as.numeric(snvs_tmp[, "DEPTH_REV"]))
       snvs_new2[new_row, "DEPTH_NORM_FWD"] = snvs_tmp[1, "DEPTH_NORM_FWD"]
       snvs_new2[new_row, "DEPTH_NORM_REV"] = snvs_tmp[1, "DEPTH_NORM_REV"]
       snvs_new2[new_row, "TIMES_CALLED"] = freq
@@ -370,13 +372,26 @@ if (num_indels > 0) {
       indels_new[new_row, "MQ"] = indels_tmp[1, "MQ"]
       indels_new[new_row, "DP4"] = indels_tmp[1, "DP4"]
       indels_new[new_row, "mut_id"] = indels_tmp[1, "mut_id"]
+
+      indels_new[new_row, "BBEG"] = paste(indels_tmp[, "BBEG"], collapse = ",")
+      indels_new[new_row, "BEND"] = paste(indels_tmp[, "BEND"], collapse = ",")
+      indels_new[new_row, "QPOS"] = paste(indels_tmp[, "QPOS"], collapse = ",")
+      indels_new[new_row, "DEPTH_FWD"] = median(as.numeric(indels_tmp[, "DEPTH_FWD"]))
+      indels_new[new_row, "DEPTH_REV"] = median(as.numeric(indels_tmp[, "DEPTH_REV"]))
+      indels_new[new_row, "DEPTH_NORM_FWD"] = indels_tmp[1, "DEPTH_NORM_FWD"]
+      indels_new[new_row, "DEPTH_NORM_REV"] = indels_tmp[1, "DEPTH_NORM_REV"]
+      indels_new[new_row, "DPLX_ASXS"] = paste(indels_tmp[, "DPLX_ASXS"], collapse = ",")
+      indels_new[new_row, "DPLX_CLIP"] = paste(indels_tmp[, "DPLX_CLIP"], collapse = ",")
+      indels_new[new_row, "DPLX_NM"] = paste(indels_tmp[, "DPLX_NM"], collapse = ",")
+      indels_new[new_row, "BULK_ASXS"] = paste(indels_tmp[, "BULK_ASXS"], collapse = ",")
+      indels_new[new_row, "BULK_NM"] = paste(indels_tmp[, "BULK_NM"], collapse = ",")
     }
   }
 
   indels_new = indels_new[order(indels_new$chr, indels_new$pos),]
 
   # drop some columns:
-  indels_new = indels_new[, c("chr", "pos", "kk", "ref", "mut", "qual", "filter", "rb_id", "TYPE", "TIMES_CALLED", "SEQ")]
+  indels_new = indels_new[, c("chr", "pos", "kk", "ref", "mut", "qual", "filter", "rb_id", "TYPE", "TIMES_CALLED", "SEQ","BBEG","BEND","QPOS","DEPTH_FWD","DEPTH_REV","DEPTH_NORM_FWD","DEPTH_NORM_REV","DPLX_ASXS","DPLX_CLIP","DPLX_NM","BULK_ASXS","BULK_NM")]
 
   ##########################################################################################
   # Calculate VAFs for indels 
@@ -468,6 +483,10 @@ if (num_indels > 0) {
   indels_final$INFO = paste(indels_final$INFO, rep("DUPLEX_VAF=", nrow(indels_final)), indels_final$DUPLEX_VAF, ";", sep = "")
   indels_final$INFO = paste(indels_final$INFO, rep("BAM_VAF=", nrow(indels_final)), indels_final$BAM_VAF, ";", sep = "")
   indels_final$INFO = paste(indels_final$INFO, rep("BAM_VAF_BQ10=", nrow(indels_final)), indels_final$BAM_VAF_BQ10, ";", sep = "")
+  indels_final$INFO = paste(indels_final$INFO, rep("DEPTH_NORM_FWD=", nrow(indels_final)), indels_final$DEPTH_NORM_FWD, ";", sep = "")
+  indels_final$INFO = paste(indels_final$INFO, rep("DEPTH_NORM_REV=", nrow(indels_final)), indels_final$DEPTH_NORM_REV, ";", sep = "")
+  indels_final$INFO = paste(indels_final$INFO, rep("DEPTH_FWD=", nrow(indels_final)), indels_final$DEPTH_FWD, ";", sep = "")
+  indels_final$INFO = paste(indels_final$INFO, rep("DEPTH_REV=", nrow(indels_final)), indels_final$DEPTH_REV, ";", sep = "")
   indels_final$INFO = paste(indels_final$INFO, rep("SEQ=", nrow(indels_final)), indels_final$SEQ, ";", sep = "")
   indels_final$INFO = paste(indels_final$INFO, rep("DUPLEX_COV=", nrow(indels_final)), indels_final$DUPLEX_COV, ";", sep = "")
   indels_final$INFO = paste(indels_final$INFO, rep("BAM_MUT=", nrow(indels_final)), indels_final$BAM_MUT, ";", sep = "")
@@ -475,6 +494,12 @@ if (num_indels > 0) {
   indels_final$INFO = paste(indels_final$INFO, rep("BAM_MUT_BQ10=", nrow(indels_final)), indels_final$BAM_MUT_BQ10, ";", sep = "")
   indels_final$INFO = paste(indels_final$INFO, rep("BAM_COV_BQ10=", nrow(indels_final)), indels_final$BAM_COV_BQ10, ";", sep = "")
   indels_final$INFO = paste(indels_final$INFO, rep("RB=", nrow(indels_final)), indels_final$rb_id, "", sep = "")
+  indels_final$INFO = paste(indels_final$INFO, rep("QPOS=", nrow(indels_final)), indels_final$QPOS, ";", sep = "")
+  indels_final$INFO = paste(indels_final$INFO, rep("DPLX_ASXS=", nrow(indels_final)), indels_final$DPLX_ASXS, ";", sep = "")
+  indels_final$INFO = paste(indels_final$INFO, rep("DPLX_CLIP=", nrow(indels_final)), indels_final$DPLX_CLIP, ";", sep = "")
+  indels_final$INFO = paste(indels_final$INFO, rep("DPLX_NM=", nrow(indels_final)), indels_final$DPLX_NM, ";", sep = "")
+  indels_final$INFO = paste(indels_final$INFO, rep("BULK_ASXS=", nrow(indels_final)), indels_final$BULK_ASXS, ";", sep = "")
+  indels_final$INFO = paste(indels_final$INFO, rep("BULK_NM=", nrow(indels_final)), indels_final$BULK_NM, "", sep = "")
 }
 
 # Describe in header:
diff --git a/perl/indelCaller_step1.pl b/perl/indelCaller_step1.pl
index bff32b6..18672d9 100755
--- a/perl/indelCaller_step1.pl
+++ b/perl/indelCaller_step1.pl
@@ -109,8 +109,9 @@
   my $bulk_rev = $bulkReverseTotal;
   next if($bulk_fwd + $bulk_rev < $bulk_min_cov); # Bulk minimum coverage
   next if($dplxCLIP > $max_clip);
-  next if($dplxNM > 20); # made very liberal to allow long indels. Check the impact!
+  next if($dplxNM > 20); # made very liberal to allow long indels. Check the impact! --> it seems is working, good
   next if($dplxASXS < $min_asxs || $bulkASXS < $min_asxs ); #fa8: fixed bug, we needed to check AS-XS for the bulk too
+  															#     Fixed but: from bitwise OR to logical OR (ainsss)
 
   if($r1 >= $min_size_subfam && $r2 >= $min_size_subfam) {
     my $bulktotal = $bulkForwardTotal+$bulkReverseTotal;
@@ -152,7 +153,17 @@
       $signature_trinuc = &reverse_signature($signature_trinuc);
     }
     $site_tags .= "$signature_trinuc;SW=$shearwater;cSNP=$commonSNP";
-
+    $site_tags .= ";BBEG=$dplxBreakpointBeg";
+    $site_tags .= ";BEND=$dplxBreakpointEnd";
+    $site_tags .= ";DEPTH_FWD=$r1";
+    $site_tags .= ";DEPTH_REV=$r2";
+    $site_tags .= ";DEPTH_NORM_FWD=$bulkForwardTotal";
+    $site_tags .= ";DEPTH_NORM_REV=$bulkReverseTotal";
+    $site_tags .= ";DPLX_ASXS=$dplxASXS";
+    $site_tags .= ";DPLX_CLIP=$dplxCLIP";
+    $site_tags .= ";DPLX_NM=$dplxNM";
+    $site_tags .= ";BULK_ASXS=$bulkASXS";
+    $site_tags .= ";BULK_NM=$bulkNM";
     # If seen in the bulk, flag it:
     if($bulkForwardIndel+$bulkReverseIndel > $max_vaf * $bulktotal) {
       $site_tags .= ";BULK_SEEN($dplxForwardIndel+$dplxReverseIndel/$bulktotal)";
diff --git a/perl/indelCaller_step2.pl b/perl/indelCaller_step2.pl
index 682dbcd..141a9d8 100755
--- a/perl/indelCaller_step2.pl
+++ b/perl/indelCaller_step2.pl
@@ -114,6 +114,7 @@ sub cmp_chr {
 
 sub runCmd {
   my $cmd = $_[0];
+  print STDERR "$cmd\n";
   my ($stdout, $stderr, $exit) = capture {
     system($cmd);
   };
@@ -126,11 +127,17 @@ sub runCmd {
 my %ignore_indels_at;
 while(<IN>) { # input bed files are generated by indelCaller.pl [step 1]
   my($chr,$pos0,$pos1,$info)             = (split(/\t/,$_  ))[0,1,2,3]    ;
-  my($rb_id,$dp,$qpos,$context,$sw,$snp) = (split(/;/,$info))[0,1,2,3,4,5];
+  my($rb_id,$dp,$qpos,$context,$sw,$snp,
+     $bbeg,$bend,$depth_fwd,$depth_rev,
+     $depth_norm_fwd,$depth_norm_rev,
+     $dplxASXS,$dplxCLIP,$dplxNM,
+     $bulkASXS,$bulkNM)                  = (split(/;/,$info))[0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16];
   if( /BULK_SEEN/ ) { #filter if site comes from the bulk sample
      $ignore_indels_at{$chr}->{$pos1} = 1;
      next;
   }
+
+
   chomp;
   #my @tmp = split(/[:\-\|]/,$rb_id);
   my @tmp1 = split(/[:\-]/,$rb_id);
@@ -142,11 +149,22 @@ sub runCmd {
   $rb_id  = "@tmp";
   $sw     =~ s/SW=//;
   $snp    =~ s/cSNP=//;
-  $indels{$rb_id}->{$pos1}->{"dp"     }  = $dp     ;
-  $indels{$rb_id}->{$pos1}->{"qpos"   }  = $qpos   ;
-  $indels{$rb_id}->{$pos1}->{"context"}  = $context;
-  $indels{$rb_id}->{$pos1}->{"sw"     }  = $sw     ;
-  $indels{$rb_id}->{$pos1}->{"snp"    }  = $snp    ;
+  $indels{$rb_id}->{$pos1}->{"dp"            }  = $dp              ;
+  $indels{$rb_id}->{$pos1}->{"qpos"          }  = $qpos            ;
+  $indels{$rb_id}->{$pos1}->{"context"       }  = $context         ;
+  $indels{$rb_id}->{$pos1}->{"sw"            }  = $sw              ;
+  $indels{$rb_id}->{$pos1}->{"snp"           }  = $snp             ;
+  $indels{$rb_id}->{$pos1}->{"bbeg"          }  = $bbeg            ;
+  $indels{$rb_id}->{$pos1}->{"bend"          }  = $bend            ;
+  $indels{$rb_id}->{$pos1}->{"depth_fwd"     }  = $depth_fwd       ;
+  $indels{$rb_id}->{$pos1}->{"depth_rev"     }  = $depth_rev       ;
+  $indels{$rb_id}->{$pos1}->{"depth_norm_fwd"}  = $depth_norm_fwd  ;
+  $indels{$rb_id}->{$pos1}->{"depth_norm_rev"}  = $depth_norm_rev  ;
+  $indels{$rb_id}->{$pos1}->{"dplxASXS"      }  = $dplxASXS        ;
+  $indels{$rb_id}->{$pos1}->{"dplxCLIP"      }  = $dplxCLIP        ;
+  $indels{$rb_id}->{$pos1}->{"dplxNM"        }  = $dplxNM          ;
+  $indels{$rb_id}->{$pos1}->{"bulkASXS"      }  = $bulkASXS        ;
+  $indels{$rb_id}->{$pos1}->{"bulkNM"        }  = $bulkNM          ;
   $counts++;
 }
 print STDOUT "$counts indel sites seen\n";
@@ -212,6 +230,7 @@ sub runCmd {
     $get_header = 1;
   }
   print STDOUT "\nChecking result\n";
+  print STDOUT "Step 7...\n";
   open(IN_TMP, "<$tempdir/$out_name.tmp2.vcf") or die "Couldn't open $tempdir/$out_name.tmp2.vcf\n";
   my @info = ();
   my $count = 0;
@@ -224,6 +243,19 @@ sub runCmd {
         if ($once and /^##FORMAT/){
           $_ = "##FILTER=<ID=MASKED,Description=\"Site overlaps with SW or SNP site\">\n" . $_;
           $_ = "##INFO=<ID=RB,Number=1,Type=String,Description=\"Readbundle ID\">\n" . $_ ;
+##INFO=<ID=RB,Number=1,Type=String,Description="Readbundle ID">
+		  $_ = "##INFO=<ID=QPOS,Number=1,Type=Integer,Description=\"Read position\">\n" . $_ ;
+		  $_ = "##INFO=<ID=BBEG,Number=1,Type=Integer,Description=\"Start breakpoint\">\n" . $_ ;
+		  $_ = "##INFO=<ID=BEND,Number=1,Type=Integer,Description=\"End breakpoing\">\n" . $_ ;
+		  $_ = "##INFO=<ID=DEPTH_FWD,Number=1,Type=Integer,Description=\"Depth RB forward\">\n" . $_ ;
+		  $_ = "##INFO=<ID=DEPTH_REV,Number=1,Type=String,Description=\"Depth RB reverse\">\n" . $_ ;
+		  $_ = "##INFO=<ID=DEPTH_NORM_FWD,Number=1,Type=Integer,Description=\"Depth normal forward\">\n" . $_ ;
+		  $_ = "##INFO=<ID=DEPTH_NORM_REV,Number=1,Type=Integer,Description=\"Depth normal reverse\">\n" . $_ ;
+		  $_ = "##INFO=<ID=DPLX_ASXS,Number=1,Type=Float,Description=\"RB mean AS-XS\">\n" . $_ ;
+		  $_ = "##INFO=<ID=DPLX_CLIP,Number=1,Type=Float,Description=\"RB mean CLIP\">\n" . $_ ;
+		  $_ = "##INFO=<ID=DPLX_NM,Number=1,Type=Float,Description=\"RB mean NM\">\n" . $_ ;
+		  $_ = "##INFO=<ID=BULK_ASXS,Number=1,Type=Float,Description=\"Normal mean AS-XS\">\n" . $_ ;
+		  $_ = "##INFO=<ID=BULK_NM,Number=1,Type=Float,Description=\"Normal mean NM\">\n" . $_ ;
           $once = 0;
         }
         if ( /^#CHROM/ ){ #use a simple sample name, without path
@@ -249,8 +281,23 @@ sub runCmd {
       next;
     }
     print "RESULT: $_\n";
-    my @fields = split(/\t/,$_);
-    $fields[7] = "$fields[7];RB=$rb_id";
+    my @fields          = split(/\t/,$_);
+    print STDERR "fields=@fields\n";
+    my $anyisok         = (keys(%{$indels{$rb_id}}))[0];
+    my $qpos            = $indels{$rb_id}->{$anyisok}->{"qpos"          };
+    my $bbeg            = $indels{$rb_id}->{$anyisok}->{"bbeg"          };
+	my $bend            = $indels{$rb_id}->{$anyisok}->{"bend"          };
+	my $depth_fwd       = $indels{$rb_id}->{$anyisok}->{"depth_fwd"     };
+	my $depth_rev       = $indels{$rb_id}->{$anyisok}->{"depth_rev"     };
+	my $depth_norm_fwd  = $indels{$rb_id}->{$anyisok}->{"depth_norm_fwd"};
+	my $depth_norm_rev  = $indels{$rb_id}->{$anyisok}->{"depth_norm_rev"};
+	my $dplxASXS        = $indels{$rb_id}->{$anyisok}->{"dplxASXS"      };
+	my $dplxCLIP        = $indels{$rb_id}->{$anyisok}->{"dplxCLIP"      };
+	my $dplxNM          = $indels{$rb_id}->{$anyisok}->{"dplxNM"        };
+	my $bulkASXS        = $indels{$rb_id}->{$anyisok}->{"bulkASXS"      };
+	my $bulkNM          = $indels{$rb_id}->{$anyisok}->{"bulkNM"        };
+    #$fields[7] = "$fields[7];QPOS=$qpos;RB=$rb_id;BBEG=$bbeg;BEND=$bend;DEPTH_FWD=$depth_fwd;DEPTH_REV=$depth_rev;DEPTH_NORM_FWD=$depth_norm_fwd;DEPTH_NORM_REV=$depth_norm_rev;DPLX_ASXS=$dplxASXS;DPLX_CLIP=$dplxCLIP;DPLX_NM=$dplxNM;BULK_ASXS=$bulkASXS;BULK_NM=$bulkNM";
+    $fields[7] = "$fields[7];$qpos;RB=$rb_id;$bbeg;$bend;$depth_fwd;$depth_rev;$depth_norm_fwd;$depth_norm_rev;$dplxASXS;$dplxCLIP;$dplxNM;$bulkASXS;$bulkNM";
     $fields[6] = "PASS";
     # If there is overlap with SW or cSNP, flag it as MASKED
     # fa8: Do this only when the overlap is significant? If not, very long deletions are likely to overlap
@@ -265,6 +312,7 @@ sub runCmd {
 	    $fields[6] = "MASKED";
     }
     $info[$count] = join "\t",@fields;
+    print STDERR "$count: @fields\n";
     # fa8: check if it's in the list of ignore_indels_at{chr}->{pos}
     for(my $i=$fields[1]; $i<= ($fields[1] + length($fields[3])); $i++) {
       if(exists($ignore_indels_at{$fields[0]}->{$i})) {
@@ -287,6 +335,7 @@ sub runCmd {
                                                                        # to:
                                                                        #   my $best_count = 0;
 }
+print STDOUT "Step 8...\n";
 if (  $header eq "") { #minimal header for an empty vcf
   print OUT "##fileformat=VCFv4.2\n#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\t$sample_name\n"; 
   OUT->flush();