diff --git a/alignment/abra2.sh b/alignment/abra2.sh
new file mode 100755
index 0000000000000000000000000000000000000000..173fdfa17ce6ee394e6a0a74e12eeb9eda187edc
--- /dev/null
+++ b/alignment/abra2.sh
@@ -0,0 +1,58 @@
+#!/bin/bash
+#gatkrunner.sh
+
+usage() {
+  echo "-h Help documentation for gatkrunner.sh"
+  echo "-r  --Reference Genome: GRCh38 or GRCm38"
+  echo "-b  --BAM File"
+  echo "-p  --Prefix for output file name"
+  echo "-a  --Algorithm/Command"
+  echo "Example: bash hisat.sh -p prefix -r GRCh38 -b File.bam"
+  exit 1
+}
+OPTIND=1 # Reset OPTIND
+while getopts :r:a:c:b:p:h opt
+do
+    case $opt in
+        r) index_path=$OPTARG;;
+        b) sbam=$OPTARG;;
+        p) pair_id=$OPTARG;;
+	c) tbed=$OPTARG;;
+        h) usage;;
+    esac
+done
+
+shift $(($OPTIND -1))
+
+# Check for mandatory options
+if [[ -z $pair_id ]] || [[ -z $sbam ]] || [[ -z $index_path ]]
+then
+    usage
+fi
+
+NPROC=$SLURM_CPUS_ON_NODE
+if [[ -z $NPROC ]]
+then
+    NPROC=`nproc`
+fi
+
+if [[ -z $isdocker ]]
+then
+    source /etc/profile.d/modules.sh
+    module load abra2/2.18 samtools/gcc/1.8
+    abrajar=/cm/shared/apps/abra2/lib/abra2.jar
+else
+    abrajar=/usr/local/bin/abra2.jar
+fi
+ioopt="--in ${sbam} --out ${pair_id}.abra2.bam"
+opt=''
+if [ -n "$tbed" ]
+then
+    opt="--targets $tbed"
+fi
+
+which samtools
+samtools index -@ $NPROC ${sbam}
+mkdir tmpdir
+java -Xmx16G -jar ${abrajar} ${ioopt} --ref ${index_path}/genome.fa --threads $NPROC $opt --tmpdir tmpdir --mbq 150 --mnf 5 --mer 0.05 > abra.log
+samtools index -@ $NPROC ${pair_id}.abra2.bam
diff --git a/alignment/bam2tdf.sh b/alignment/bam2tdf.sh
index e6299d58137337fa2ded981c5239809c2ecf8e43..1834c773216b5d39c48dbe346a7f1ba16eaa51ac 100755
--- a/alignment/bam2tdf.sh
+++ b/alignment/bam2tdf.sh
@@ -30,8 +30,10 @@ then
 fi
 
 baseDir="`dirname \"$0\"`"
-
-source /etc/profile.d/modules.sh
-module load igvtools/2.3.71 samtools/1.6
+if [[ -z $isdocker ]]
+then
+    source /etc/profile.d/modules.sh
+    module load igvtools/2.3.71 samtools/1.6
+exit
 samtools index  -@ $NPROC $bam
 igvtools count -z 5 $bam ${pair_id}.tdf ${index_path}/igv/human.genome
diff --git a/alignment/hisat_genotype.sh b/alignment/hisat_genotype.sh
index 4ee37c672dea6910e9f0a8e9b8516e55ed4d35b6..97e3f719ceb3f9cdfcec8461225220fd7a91a0eb 100755
--- a/alignment/hisat_genotype.sh
+++ b/alignment/hisat_genotype.sh
@@ -35,9 +35,11 @@ then
     NPROC=`nproc`
 fi
 
-source /etc/profile.d/modules.sh
-module load hisat-genotype/1.0.1
-
+if [[ -z $isdocker ]]
+then
+    source /etc/profile.d/modules.sh
+    module load hisat-genotype/1.0.1
+fi
 diff $fq1 $fq2 > difffile
 
 if [ -s difffile ]
diff --git a/alignment/indexbams.sh b/alignment/indexbams.sh
index 2af125dd027eac1ad1ae2cefd1f776e0a9bc17a5..ecdab135ba10b8bbe7e2b9dee4e4db59577f421d 100755
--- a/alignment/indexbams.sh
+++ b/alignment/indexbams.sh
@@ -26,8 +26,12 @@ fi
 
 baseDir="`dirname \"$0\"`"
 
-source /etc/profile.d/modules.sh
-module load samtools/1.6
+if [[ -z $isdocker ]]
+then
+    source /etc/profile.d/modules.sh
+    module load samtools/1.6
+fi
+
 for i in *.bam; do
     samtools index -@ $NPROC ${i}
 done 
diff --git a/alignment/starfusion.sh b/alignment/starfusion.sh
index 9bc7050514e97f7443c57425a51cad3aac6491ef..e60b0b85dbaccf1df77a7a6c2177d082f3798c6a 100755
--- a/alignment/starfusion.sh
+++ b/alignment/starfusion.sh
@@ -43,10 +43,6 @@ if [[ -z $isdocker ]]
 then
     source /etc/profile.d/modules.sh
     module add python/2.7.x-anaconda star/2.5.2b bedtools/2.26.0
-fi
-
-if [[ -n $method ]] && [[ $method == 'trinity' ]]
-then
     module load trinity/1.6.0
     tmphome="/tmp/$USER"
     if [[ -z $tmphome ]]
diff --git a/genect_rnaseq/geneabundance.sh b/genect_rnaseq/geneabundance.sh
index bbaf11f1e923f6d46f218987b7a12696e7b00411..b8e8fdb37bea875b3d87c086f9f172c598222a3b 100644
--- a/genect_rnaseq/geneabundance.sh
+++ b/genect_rnaseq/geneabundance.sh
@@ -44,9 +44,9 @@ if [[ -z $isdocker ]]
 then
     source /etc/profile.d/modules.sh
     module load subread/1.6.1
+    export PATH=/project/shared/bicf_workflow_ref/seqprg/bin:$PATH
 fi
 baseDir="`dirname \"$0\"`"
-export PATH=/project/shared/bicf_workflow_ref/seqprg/bin:$PATH
 
 featureCounts -s $stranded -M --fraction -J --ignoreDup -T $NPROC -p -g gene_name -a ${gtf} -o ${pair_id}.cts ${sbam}
 
diff --git a/genect_rnaseq/statanal.sh b/genect_rnaseq/statanal.sh
index 23efcf1a0d71687ffbee469dec947b63228cbaeb..cdf3b1cc3bff190c25dc9cd332e9caf2efad399e 100644
--- a/genect_rnaseq/statanal.sh
+++ b/genect_rnaseq/statanal.sh
@@ -25,8 +25,10 @@ if [[ -z $NPROC ]]
 then
     NPROC=`nproc`
 fi
-source /etc/profile.d/modules.sh
-
+if [[ -z $isdocker ]]
+then
+    source /etc/profile.d/modules.sh
+fi
 perl $baseDir/concat_cts.pl -o ./ *.cts
 perl $baseDir/concat_fpkm.pl -o ./ *.fpkm.txt
 perl $baseDir/concat_ctsum.pl -o ./ *.cts.summary
diff --git a/variants/itdseek.sh b/obsolete/itdseek.sh
similarity index 100%
rename from variants/itdseek.sh
rename to obsolete/itdseek.sh
diff --git a/variants/pindel.sh b/obsolete/pindel.sh
similarity index 100%
rename from variants/pindel.sh
rename to obsolete/pindel.sh
diff --git a/variants/checkmate.sh b/variants/checkmate.sh
index 855b168723c48b383dd3e328c72a715a54959171..ddd70c2be2c69f34d99d18a0741d3c0594a38c61 100755
--- a/variants/checkmate.sh
+++ b/variants/checkmate.sh
@@ -33,9 +33,9 @@ then
     source /etc/profile.d/modules.sh	
     module load samtools/gcc/1.8 bcftools/gcc/1.8
     ncm=/project/shared/bicf_workflow_ref/seqprg/NGSCheckMate/ncm.py
+    export PATH=/project/shared/bicf_workflow_ref/seqprg/bin:$PATH
 fi
 
-export PATH=/project/shared/bicf_workflow_ref/seqprg/bin:/usr/local/bin/:$PATH
 if [[ -f /usr/local/bin/ncm.py ]]
 then
     ncm=/usr/local/bin/ncm.py
diff --git a/variants/filter_pindel.pl b/variants/filter_pindel.pl
index 1802a79e5c8b8dd01f9f5ad1fe472afb96bf7784..0048d753d422539d514ce499826665feb87a2741 100755
--- a/variants/filter_pindel.pl
+++ b/variants/filter_pindel.pl
@@ -43,7 +43,7 @@ foreach $file (@files) {
       $hash{$key} = $val unless ($hash{$key});
     }
     next unless ($hash{ANN});
-    next unless ($hash{ANN} =~ m/HIGH|MODERATE|LOW/);
+    #next unless ($hash{ANN} =~ m/HIGH|MODERATE|LOW/);
     my %gtinfo = ();
     my @deschead = split(/:/,$format);
   F1:foreach my $k (0..$#gtheader) {
@@ -79,15 +79,15 @@ foreach $file (@files) {
     @tumoraltct = split(/,/,$gtinfo{$opt{tumor}}{AO});
     next if ($tumoraltct[0] eq '.');
     $hash{AF} = join(",",@tumormaf);
-    next if ($tumoraltct[0] < 20);
+    next if ($tumoraltct[0] < 20 && $tumormaf[0] < 0.05);
     next if ($tumormaf[0] < 0.01);
     my $keepforvcf = 0;
     foreach $trx (split(/,/,$hash{ANN})) {
       my ($allele,$effect,$impact,$gene,$geneid,$feature,
 	  $featureid,$biotype,$rank,$codon,$aa,$pos_dna,$len_cdna,
 	  $cds_pos,$cds_len,$aapos,$aalen,$distance,$err) = split(/\|/,$trx);
-      next unless ($impact =~ m/HIGH|MODERATE/ || $effect =~ /splice/i);
-      next if($effect eq 'sequence_feature');
+      #next unless ($impact =~ m/HIGH|MODERATE/ || $effect =~ /splice/i);
+      #next if($effect eq 'sequence_feature');
       $keepforvcf = $gene;
     }
     next unless $keepforvcf;
diff --git a/variants/filter_svaba.pl b/variants/filter_svaba.pl
index e9625704e8fae361f70d8c1218f254c6ba5fffe6..72a2eb390ab8679f0a41e0bb4c46ee146db05c7f 100755
--- a/variants/filter_svaba.pl
+++ b/variants/filter_svaba.pl
@@ -41,11 +41,11 @@ W1:while (my $line = <IN>) {
     $hash{$key} = $val unless ($hash{$key});
   }
   if (length($alt) > length($ref)) {
-      $hash{SVTYPE} = "INS";
-      $hash{END} = $pos;
+    $hash{SVTYPE} = "INS";
+    $hash{END} = $pos;
   }elsif (length($alt) < length($ref)) {
-      my $diff = substr($ref, length($alt));
-      $hash{SVTYPE} = "DEL";
+    my $diff = substr($ref, length($alt));
+    $hash{SVTYPE} = "DEL";
       $hash{END} = $pos + length($diff);
   }
   next unless ($hash{ANN});
@@ -92,7 +92,7 @@ W1:while (my $line = <IN>) {
     my ($allele,$effect,$impact,$gene,$geneid,$feature,
 	$featureid,$biotype,$rank,$codon,$aa,$pos_dna,$len_cdna,
 	$cds_pos,$cds_len,$aapos,$aalen,$distance,$err) = split(/\|/,$trx);
-    next unless ($impact =~ m/HIGH|MODERATE/ || $effect =~ /splice/i);
+    next unless ($impact =~ m/HIGH|MODERATE|LOW/ || $effect =~ /splice/i);
     next if($effect eq 'sequence_feature');
     $keeptrx = $trx;
     $keepforvcf = $gene;
@@ -107,7 +107,6 @@ W1:while (my $line = <IN>) {
       push @nannot, $info;
     }
   }
-  
   my $newannot = join(";",@nannot);
   if ($hash{SVTYPE} eq 'INS' || ($hash{SVTYPE} eq 'DEL' && $keepforvcf !~ m/&/)) {
     if ($filter =~ m/LOWMAPQ|LowQual/i) {
@@ -231,9 +230,6 @@ close IN;
 
 
 foreach my $id (keys %svpairs) {
-  if ($id =~ m/815016443/) {
-      warn "debugging\n";
-  }
   my $alt1 = $svpairs{$id}{1}{alt};
   my $alt2 = $svpairs{$id}{2}{alt};
   my $svtype;
@@ -242,14 +238,14 @@ foreach my $id (keys %svpairs) {
   }elsif ($alt2 =~ m/^\w\[/ && $alt1 =~ m/^\]/) {
     $svtype = 'INS';
   }else {
-      $svtype = 'UNK';
+    $svtype = 'UNK';
   }
-   if ($svtype eq 'INS' || ($svtype eq 'DEL' && $svpairs{$id}{1}{gene} !~ m/&/ && $svpairs{$id}{1}{span} < 9999)) {
-     if ($filter =~ m/LOWMAPQ|LowQual/i) {
+  if ($svtype eq 'INS' || ($svtype eq 'DEL' && $svpairs{$id}{1}{gene} !~ m/&/ && $svpairs{$id}{1}{span} < 9999)) {
+    if ($filter =~ m/LOWMAPQ|LowQual/i) {
       $filter = 'FailedQC'.$filter;
-    }
+      }
     print VCFOUT $svpairs{$id}{1}{vcfline},"\n"
-   }elsif ($svtype eq 'DEL' && $svpairs{$id}{1}{span} && $svpairs{$id}{1}{span} > 9999) {
-     print DELFUS $svpairs{$id}{1}{fusionline},"\n";
-   }
+  }elsif ($svtype eq 'DEL' && $svpairs{$id}{1}{span} && $svpairs{$id}{1}{span} > 9999) {
+    print DELFUS $svpairs{$id}{1}{fusionline},"\n";
+  }
 }
diff --git a/variants/germline_vc.sh b/variants/germline_vc.sh
index a4ff47e47d4e3ec6ef953a04d4f1e41affc8c648..334d7d691a2cb1312d4454f270c1c757b4835284 100755
--- a/variants/germline_vc.sh
+++ b/variants/germline_vc.sh
@@ -107,6 +107,12 @@ then
     fi
     bamlist=`join_by , *.bam`
     Platypus.py callVariants --minMapQual=0 --minReads=3 --mergeClusteredVariants=1 --nCPU=$NPROC --bamFiles=${bamlist} --refFile=${reffa} --output=platypus.vcf
+    for i in *.bam
+    do
+	prefix="${i%.bam}"
+	sid=`samtools view -H ${i} |grep '^@RG' |perl -pe 's/\t/\n/g' |grep ID |cut -f 2 -d ':'`
+	perl -pi -e "s/$prefix/$sid/g" platypus.vcf
+    done
     vcf-sort platypus.vcf |vcf-annotate -n --fill-type -n |bgzip > platypus.vcf.gz
     tabix platypus.vcf.gz
     bcftools norm -c s -f ${reffa} -w 10 -O z -o ${pair_id}.platypus.vcf.gz platypus.vcf.gz
diff --git a/variants/msisensor.sh b/variants/msisensor.sh
index 1d27dc83ee69e9e9f586c93263c4511817470d6a..c2e59167eb7062a60adf5a1d9026e006a543bfdc 100755
--- a/variants/msisensor.sh
+++ b/variants/msisensor.sh
@@ -30,8 +30,10 @@ if [[ -z $sbam ]] || [[ -z $index_path ]]; then
     usage
 fi
 
-export PATH=/project/shared/bicf_workflow_ref/seqprg/bin:$PATH
-
+if [[ -z $isdocker ]]
+then
+    export PATH=/project/shared/bicf_workflow_ref/seqprg/bin:$PATH
+fi
 bedopt=''
 if [[ -n $capture ]]
 then
diff --git a/variants/norm_annot.sh b/variants/norm_annot.sh
index 776c306c6bae5c965e07f648b16ecf1554e14194..d282231782066cac93e8b0c7d3283cfc98718291 100755
--- a/variants/norm_annot.sh
+++ b/variants/norm_annot.sh
@@ -24,8 +24,11 @@ function join_by { local IFS="$1"; shift; echo "$*"; }
 shift $(($OPTIND -1))
 baseDir="`dirname \"$0\"`"
 
-source /etc/profile.d/modules.sh
-module load bedtools/2.26.0 samtools/gcc/1.8 bcftools/gcc/1.8 snpeff/4.3q 
+if [[ -z $isdocker ]]
+then
+    source /etc/profile.d/modules.sh
+    module load bedtools/2.26.0 samtools/gcc/1.8 bcftools/gcc/1.8 snpeff/4.3q 
+fi
 
 if [[ -a "${index_path}/genome.fa" ]]
 then
diff --git a/variants/somatic_vc.sh b/variants/somatic_vc.sh
index 9923e359071c4e28521bc4e1b002bd5c7303685d..95deb660d21fbf1f74c83dbf15269eeba2be02b3 100755
--- a/variants/somatic_vc.sh
+++ b/variants/somatic_vc.sh
@@ -38,8 +38,8 @@ if [[ -z $isdocker ]]
 then
     source /etc/profile.d/modules.sh
     module load htslib/gcc/1.8 samtools/gcc/1.8 snpeff/4.3q vcftools/0.1.14
+    export PATH=/project/shared/bicf_workflow_ref/seqprg/bin:$PATH
 fi
-export PATH=/project/shared/bicf_workflow_ref/seqprg/bin:$PATH
 
 shift $(($OPTIND -1))
 
diff --git a/variants/svcalling.sh b/variants/svcalling.sh
index b01363fa80861ac48be8728d8244b78cbaeeb4b6..562d2eefe3344a6bae29089cada98d1f378a1be6 100755
--- a/variants/svcalling.sh
+++ b/variants/svcalling.sh
@@ -62,18 +62,23 @@ if [[ -z $isdocker ]]
 then
     source /etc/profile.d/modules.sh	
     module load htslib/gcc/1.8 samtools/gcc/1.8 bcftools/gcc/1.8 bedtools/2.26.0 snpeff/4.3q vcftools/0.1.14
+    export PATH=/project/shared/bicf_workflow_ref/seqprg/bin:$PATH
 fi
-export PATH=/project/shared/bicf_workflow_ref/seqprg/bin:$PATH
 mkdir -p temp
 
-if [[ -z $tid ]]
+if [[ -z $tid ]] && [[ -f ${sbam} ]]
 then
     tid=`samtools view -H ${sbam} |grep '^@RG' |perl -pe 's/\t/\n/g' |grep ID |cut -f 2 -d ':'`
 fi
 
 bams=''
 for i in *.bam; do
-    bams="$bams $i" 
+    bams="$bams $i"
+    sid=`samtools view -H ${i} |grep '^@RG' |perl -pe 's/\t/\n/g' |grep ID |cut -f 2 -d ':'`
+    if [[ $sid =~ "_T_" ]]
+    then
+	tid=$sid
+    fi
 done
 
 #RUN DELLY
@@ -90,8 +95,9 @@ then
     java -jar $SNPEFF_HOME/SnpSift.jar filter "( GEN[*].DP >= 20 )" ${pair_id}.delly.sv.norm.vcf.gz | java -Xmx10g -jar $SNPEFF_HOME/snpEff.jar -no-intergenic -lof -c $SNPEFF_HOME/snpEff.config ${snpeffgeno} - | bgzip > ${pair_id}.delly.vcf.gz
     if [[ $filter == 1 ]]
     then
-	zcat ${pair_id}.delly.vcf.gz | $SNPEFF_HOME/scripts/vcfEffOnePerLine.pl |java -jar $SNPEFF_HOME/SnpSift.jar extractFields - CHROM POS CHR2 END ANN[*].EFFECT ANN[*].GENE ANN[*].BIOTYPE FILTER FORMAT GEN[*] |grep -E 'gene_fusion|feature_fusion' | sort -u > ${pair_id}.dgf.txt
+	zcat ${pair_id}.delly.vcf.gz | $SNPEFF_HOME/scripts/vcfEffOnePerLine.pl |java -jar $SNPEFF_HOME/SnpSift.jar extractFields - CHROM POS CHR2 END ANN[*].EFFECT ANN[*].GENE ANN[*].BIOTYPE FILTER FORMAT GEN[*] |grep -E 'gene_fusion|feature_fusion|transcript_ablation' | sort -u > ${pair_id}.dgf.txt
 	mv ${pair_id}.delly.vcf.gz ${pair_id}.delly.ori.vcf.gz
+	echo "perl $baseDir/filter_delly.pl -t $tid -p $pair_id -i ${pair_id}.delly.ori.vcf.gz"
 	perl $baseDir/filter_delly.pl -t $tid -p $pair_id -i ${pair_id}.delly.ori.vcf.gz
 	bgzip -f ${pair_id}.delly.vcf
 	zgrep '#CHROM' ${pair_id}.delly.vcf.gz > ${pair_id}.delly.genefusion.txt
@@ -120,7 +126,7 @@ then
 
     if [[ $filter == 1 ]]
     then
-	zcat ${pair_id}.svaba.sv.vcf.gz | $SNPEFF_HOME/scripts/vcfEffOnePerLine.pl |java -jar $SNPEFF_HOME/SnpSift.jar extractFields - CHROM POS ALT ID ANN[*].EFFECT ANN[*].GENE ANN[*].BIOTYPE FILTER FORMAT GEN[*] |grep -E 'gene_fusion|feature_fusion' | sort -u  > ${pair_id}.sgf.txt
+	zcat ${pair_id}.svaba.sv.vcf.gz | $SNPEFF_HOME/scripts/vcfEffOnePerLine.pl |java -jar $SNPEFF_HOME/SnpSift.jar extractFields - CHROM POS ALT ID ANN[*].EFFECT ANN[*].GENE ANN[*].BIOTYPE FILTER FORMAT GEN[*] |grep -E 'gene_fusion|feature_fusion|transcript_ablation' | sort -u  > ${pair_id}.sgf.txt
 	mv ${pair_id}.svaba.vcf.gz ${pair_id}.svaba.ori.vcf.gz
 	perl $baseDir/filter_svaba.pl -t $tid -p ${pair_id} -i ${pair_id}.svaba.ori.vcf.gz -s ${pair_id}.svaba.sv.vcf.gz
 	bgzip ${pair_id}.svaba.vcf
@@ -190,6 +196,7 @@ then
 elif [[ $method == 'itdseek' ]]
 then
     stexe=`which samtools`
+    echo $stexe
     samtools view -@ $NPROC -L ${itdbed} ${sbam} | itdseek.pl --refseq ${reffa} --samtools ${stexe} --bam ${sbam} | vcf-sort | bedtools intersect -header -b ${itdbed} -a stdin | java -Xmx30g -jar $SNPEFF_HOME/SnpSift.jar filter "( LEN < 10000 )" | bgzip > ${pair_id}.itdseek.vcf.gz
     
     tabix ${pair_id}.itdseek.vcf.gz
diff --git a/variants/uni_norm_annot.sh b/variants/uni_norm_annot.sh
index 502fa0e6d9dedda6cd8567f37eed9f6c801020f0..56b45e683d5ad3a3359dc4bb1383ddf4c8b2200c 100755
--- a/variants/uni_norm_annot.sh
+++ b/variants/uni_norm_annot.sh
@@ -41,8 +41,8 @@ if [[ -z $isdocker ]]
 then
     source /etc/profile.d/modules.sh
     module load bedtools/2.26.0 samtools/1.6 bcftools/1.6 snpeff/4.3q 
+    export PATH=/project/shared/bicf_workflow_ref/seqprg/bin:$PATH
 fi
-export PATH=/project/shared/bicf_workflow_ref/seqprg/bin:$PATH
 
 perl $baseDir\/uniform_vcf_gt.pl $pair_id $vcf
 mv ${vcf} ${pair_id}.ori.vcf.gz