diff --git a/alignment/bamqc.sh b/alignment/bamqc.sh
index eefb332c8236d57b13c96f3e7526ecc77ce71602..029a921d4f13e70325c598c61321f1dcbe270eab 100644
--- a/alignment/bamqc.sh
+++ b/alignment/bamqc.sh
@@ -8,7 +8,7 @@ usage() {
   echo "-n  --NucType"
   echo "-p  --Prefix for output file name"
   echo "-c  --Capture Bedfile"
-  echo "Example: bash bamqc.sh -p prefix -r /project/shared/bicf_workflow_ref/GRCh38 -b SRR1551047.bam  -n dna -c target.bed"
+  echo "Example: bash bamqc.sh -p prefix -r /project/shared/bicf_workflow_ref/human/GRCh38 -b SRR1551047.bam  -n dna -c target.bed"
   exit 1
 }
 OPTIND=1 # Reset OPTIND
diff --git a/alignment/dnaseqalign.sh b/alignment/dnaseqalign.sh
index 36a13645df4ed85af8de20cfce189b13d0dc8dd0..9ae193d5c623bbd06626a463e5ae33904c53eaa6 100644
--- a/alignment/dnaseqalign.sh
+++ b/alignment/dnaseqalign.sh
@@ -8,7 +8,7 @@ usage() {
   echo "-y  --FastQ R2"
   echo "-p  --Prefix for output file name"
   echo "-u  --UMI"
-  echo "Example: bash dnaseqalign.sh -p prefix -u 1 -r /project/shared/bicf_workflow_ref/GRCh38 -x SRR1551047_1.fastq.gz  -y SRR1551047_2.fastq.gz"
+  echo "Example: bash dnaseqalign.sh -p prefix -u 1 -r /project/shared/bicf_workflow_ref/human/GRCh38 -x SRR1551047_1.fastq.gz  -y SRR1551047_2.fastq.gz"
   exit 1
 }
 OPTIND=1 # Reset OPTIND
diff --git a/alignment/filter_genefusions.pl b/alignment/filter_genefusions.pl
index f44cf58f34f07ec90b277e1944f3e8ffd042f271..1c43cd37dc9f9d66b2317a7626756454d96754e3 100755
--- a/alignment/filter_genefusions.pl
+++ b/alignment/filter_genefusions.pl
@@ -14,13 +14,13 @@ while (my $line = <ENT>) {
       $entrez{$row[2]} = $row[1];
   }
 }
-open OM, "</project/shared/bicf_workflow_ref/GRCh38/clinseq_prj/utswv2_known_genefusions.txt" or die $!;
+open OM, "</project/shared/bicf_workflow_ref/human/GRCh38/clinseq_prj/utswv2_known_genefusions.txt" or die $!;
 while (my $line = <OM>) {
     chomp($line);
     $known{$line} = 1;
 }
 close OM;
-open OM, "</project/shared/bicf_workflow_ref/GRCh38/clinseq_prj/panel1410.genelist.txt" or die $!;
+open OM, "</project/shared/bicf_workflow_ref/human/GRCh38/clinseq_prj/panel1410.genelist.txt" or die $!;
 while (my $line = <OM>) {
     chomp($line);
     $keep{$line} = 1;
diff --git a/alignment/markdups.sh b/alignment/markdups.sh
index 6338711781e0a833b01ce822de173562ffe49eeb..b794b25c4e26a1691252dce8ea5cae323f621b8e 100644
--- a/alignment/markdups.sh
+++ b/alignment/markdups.sh
@@ -63,7 +63,7 @@ then
     samtools fastq -1 ${pair_id}.consensus.R1.fastq -2 ${pair_id}.consensus.R2.fastq ${pair_id}.consensus.bam
     gzip ${pair_id}.consensus.R1.fastq
     gzip ${pair_id}.consensus.R2.fastq
-    bwa mem -M -C -t 2 -R "@RG\tID:${pair_id}\tLB:tx\tPL:illumina\tPU:barcode\tSM:${pair_id}" /project/shared/bicf_workflow_ref/GRCh38/genome.fa ${pair_id}.consensus.R1.fastq.gz ${pair_id}.consensus.R2.fastq.gz | samtools view -1 - > ${pair_id}.consensus.bam
+    bwa mem -M -C -t 2 -R "@RG\tID:${pair_id}\tLB:tx\tPL:illumina\tPU:barcode\tSM:${pair_id}" /project/shared/bicf_workflow_ref/human/GRCh38/genome.fa ${pair_id}.consensus.R1.fastq.gz ${pair_id}.consensus.R2.fastq.gz | samtools view -1 - > ${pair_id}.consensus.bam
     samtools sort --threads 10 -o ${pair_id}.dedup.bam ${pair_id}.consensus.bam
 else
     cp ${sbam} ${pair_id}.dedup.bam    
diff --git a/alignment/rnaseqalign.sh b/alignment/rnaseqalign.sh
index 182a738385e8c8bf3159c151a498df76ec89c2d6..606af0aa2fdd656a69d8e837d96b757a7bfcd72f 100644
--- a/alignment/rnaseqalign.sh
+++ b/alignment/rnaseqalign.sh
@@ -9,7 +9,7 @@ usage() {
   echo "-a  --Method: hisat or star"
   echo "-p  --Prefix for output file name"
   echo "-u  --UMI sequences are in FQ Read Name"
-  echo "Example: bash rnaseqalign.sh -a hisat -p prefix -u -r /project/shared/bicf_workflow_ref/GRCh38 -x SRR1551047_1.fastq.gz  -y SRR1551047_2.fastq.gz"
+  echo "Example: bash rnaseqalign.sh -a hisat -p prefix -u -r /project/shared/bicf_workflow_ref/human/GRCh38 -x SRR1551047_1.fastq.gz  -y SRR1551047_2.fastq.gz"
   exit 1
 }
 OPTIND=1 # Reset OPTIND
diff --git a/alignment/starfusion.sh b/alignment/starfusion.sh
index d462f5ad4c7e252f7d136eac6ee7dfbb1e423469..3e1ec53835531d75db5169237a59e0b74b178f63 100644
--- a/alignment/starfusion.sh
+++ b/alignment/starfusion.sh
@@ -7,7 +7,7 @@ usage() {
   echo "-a  --FastQ R1"
   echo "-b  --FastQ R2"
   echo "-p  --Prefix for output file name"
-  echo "Example: bash starfusion.sh -p prefix -r /project/shared/bicf_workflow_ref/GRCh38 -a SRR1551047_1.fastq.gz  -b SRR1551047_2.fastq.gz"
+  echo "Example: bash starfusion.sh -p prefix -r /project/shared/bicf_workflow_ref/human/GRCh38 -a SRR1551047_1.fastq.gz  -b SRR1551047_2.fastq.gz"
   exit 1
 }
 OPTIND=1 # Reset OPTIND
@@ -67,7 +67,7 @@ cut -f 5-8 ${pair_id}.starfusion.txt |perl -pe 's/\^|:/\t/g' | awk '{print "sing
 if [[ $filter == 1 ]]
 then
     cut -f 6,8 ${pair_id}.starfusion.txt |grep -v Breakpoint |perl -pe 's/\t/\n/g' |awk -F ':' '{print $1"\t"$2-1"\t"$2}' > temp.bed
-    bedtools intersect -wao -a temp.bed -b /project/shared/bicf_workflow_ref/GRCh38/cytoBand.txt |cut -f 1,2,7 > cytoband_pos.txt
+    bedtools intersect -wao -a temp.bed -b /project/shared/bicf_workflow_ref/human/GRCh38/cytoBand.txt |cut -f 1,2,7 > cytoband_pos.txt
     perl $baseDir/filter_genefusions.pl -p ${pair_id} -f ${pair_id}.starfusion.txt
 fi
 
diff --git a/genect_rnaseq/cBioPortal_documents.pl b/genect_rnaseq/cBioPortal_documents.pl
index 25a816e128df299832800f5b2cea921ce073ac62..5b672a32055bc7dc7e54bed7b67170e371d1f4ed 100644
--- a/genect_rnaseq/cBioPortal_documents.pl
+++ b/genect_rnaseq/cBioPortal_documents.pl
@@ -15,7 +15,7 @@ while (my $line = <ENT_ENS>){
   $entrez{$row[2]}=$row[1];
 }
 close ENT_ENS;
-open ENT_ENS, "</project/shared/bicf_workflow_ref/GRCh38/genenames.txt" or die $!;
+open ENT_ENS, "</project/shared/bicf_workflow_ref/human/GRCh38/genenames.txt" or die $!;
 my $gn_header = <ENT_ENS>;
 my %ensym;
 while (my $line = <ENT_ENS>){
diff --git a/variants/annotvcf.sh b/variants/annotvcf.sh
index 1f4d9720de5b41baf5b9b4dd3adaa0e807015c74..d3225209671997321d6a36d9befaa29fd842ed21 100755
--- a/variants/annotvcf.sh
+++ b/variants/annotvcf.sh
@@ -33,7 +33,7 @@ fi
 if  [[ $index_path == '/project/shared/bicf_workflow_ref/human/GRCh38' ]] 
 then
     tabix ${unionvcf}
-    bcftools annotate -Oz -a ${index_path}/gnomad.txt.gz -h ${index_path}/gnomad.header -c CHROM,POS,REF,ALT,GNOMAD_HOM,GNOMAD_AF,AF_POPMAX -o ${pair_id}.gnomad.vcf.gz ${unionvcf}
+    bcftools annotate -Oz -a ${index_path}/gnomad.txt.gz -h ${index_path}/gnomad.header -c CHROM,POS,REF,ALT,HG19_VARIANT,GNOMAD_HOM,GNOMAD_AF,AF_POPMAX -o ${pair_id}.gnomad.vcf.gz ${unionvcf}
     tabix ${pair_id}.gnomad.vcf.gz 
     bcftools annotate -Oz -a ${index_path}/repeat_regions.bed.gz -o ${pair_id}.repeat.vcf.gz --columns CHROM,FROM,TO,RepeatType -h /project/shared/bicf_workflow_ref/RepeatType.header ${pair_id}.gnomad.vcf.gz
     java -Xmx10g -jar $SNPEFF_HOME/snpEff.jar -no-downstream -no-upstream -no-intergenic -lof -c $SNPEFF_HOME/snpEff.config GRCh38.86 ${pair_id}.repeat.vcf.gz | java -jar $SNPEFF_HOME/SnpSift.jar annotate -id ${index_path}/dbSnp.vcf.gz -  | java -jar $SNPEFF_HOME/SnpSift.jar annotate -info CLNSIG,CLNDSDB,CLNDSDBID,CLNDBN,CLNREVSTAT,CLNACC ${index_path}/clinvar.vcf.gz - | java -jar $SNPEFF_HOME/SnpSift.jar annotate -info CNT ${index_path}/cosmic.vcf.gz - | java -Xmx10g -jar $SNPEFF_HOME/SnpSift.jar dbnsfp -v -db ${index_path}/dbNSFP.txt.gz - | bgzip > ${pair_id}.annot.vcf.gz
diff --git a/variants/cnvkit.sh b/variants/cnvkit.sh
index ea813fbcc17a5273e8feee0e7f29063e19d462db..743167f9393019ef33b91a60e4c6d6d76c5c84bb 100755
--- a/variants/cnvkit.sh
+++ b/variants/cnvkit.sh
@@ -26,7 +26,7 @@ done
 
 shift $(($OPTIND -1))
 
-index_path='/project/shared/bicf_workflow_ref/GRCh38/clinseq_prj/'
+index_path='/project/shared/bicf_workflow_ref/human/GRCh38/clinseq_prj/'
 
 # Check for mandatory options
 if [[ -z $pair_id ]] || [[ -z $sbam ]]; then
@@ -38,7 +38,7 @@ then
 fi
 baseDir="`dirname \"$0\"`"
 
-if [[ $capture == '/project/shared/bicf_workflow_ref/GRCh38/clinseq_prj/UTSWV2.bed' ]]
+if [[ $capture == '/project/shared/bicf_workflow_ref/human/GRCh38/clinseq_prj/UTSWV2.bed' ]]
 then 
     normals="${index_path}/UTSWV2.normals.cnn"
     targets="${index_path}/UTSWV2.cnvkit_"
@@ -64,5 +64,5 @@ cnvkit.py fix ${pair_id}.targetcoverage.cnn ${pair_id}.antitargetcoverage.cnn ${
 cnvkit.py segment ${pair_id}.cnr -o ${pair_id}.cns
 cnvkit.py call ${pair_id}.cns -o ${pair_id}.call.cns
 cnvkit.py scatter ${pair_id}.cnr -s ${pair_id}.call.cns -t --segment-color "blue" -o ${pair_id}.cnv.scatter.pdf
-cut -f 1,2,3 ${pair_id}.call.cns | grep -v chrom | bedtools intersect -wao -b /project/shared/bicf_workflow_ref/GRCh38/cytoBand.txt -a stdin |cut -f 1,2,3,7 >  ${pair_id}.cytoband.bed
+cut -f 1,2,3 ${pair_id}.call.cns | grep -v chrom | bedtools intersect -wao -b /project/shared/bicf_workflow_ref/human/GRCh38/cytoBand.txt -a stdin |cut -f 1,2,3,7 >  ${pair_id}.cytoband.bed
 perl $baseDir/filter_cnvkit.pl *.call.cns
diff --git a/variants/filter_cnvkit.pl b/variants/filter_cnvkit.pl
index b7504ad5823d209c647e3ae270f9e71df8f55f62..b4ddaccdd975d24fe37ca84d41dcac47b2e7e476 100755
--- a/variants/filter_cnvkit.pl
+++ b/variants/filter_cnvkit.pl
@@ -1,7 +1,7 @@
 #!/usr/bin/perl -w
 #parse_cnvkit_table.pl
 
-my $refdir = '/project/shared/bicf_workflow_ref/GRCh38/';
+my $refdir = '/project/shared/bicf_workflow_ref/human/GRCh38/';
 open OM, "<$refdir\/clinseq_prj/panel1410.genelist.txt" or die $!;
 while (my $line = <OM>) {
   chomp($line);
diff --git a/variants/somatic_callers.sh b/variants/somatic_callers.sh
index 4517c52fd4f30737223dba4046c057a3eb877362..1adde7ba1e9c6483965fb2523fc19eef85d591a0 100755
--- a/variants/somatic_callers.sh
+++ b/variants/somatic_callers.sh
@@ -36,7 +36,7 @@ if [[ -z $SLURM_CPUS_ON_NODE ]]
     SLURM_CPUS_ON_NODE=1
 fi
 
-index_path=/project/shared/bicf_workflow_ref/GRCh38
+index_path=/project/shared/bicf_workflow_ref/human/GRCh38
 
 genome_reference=${index_path}/genome.fa
 cosmic_reference=${index_path}/cosmic.vcf.gz
@@ -76,7 +76,7 @@ fi
 if [ $algo == 'mutect' ]
   then
     module load parallel python/2.7.x-anaconda gatk/3.8  bcftools/intel/1.3 bedtools/2.25.0 snpeff/4.2 vcftools/0.1.14
-    cut -f 1 /project/shared/bicf_workflow_ref/GRCh38/genomefile.5M.txt | parallel --delay 2 -j 10 "java -Xmx20g -jar $GATK_JAR -R ${genome_reference} -D ${dbSnp_reference} -T MuTect2 -stand_call_conf 30 -stand_emit_conf 10.0 -A FisherStrand -A QualByDepth -A VariantType -A DepthPerAlleleBySample -A HaplotypeScore -A AlleleBalance -I:tumor ${tumor}.final.bam -I:normal ${normal}.final.bam --cosmic ${cosmic} -o ${tumor}.{}.mutect.vcf -L {}"
+    cut -f 1 /project/shared/bicf_workflow_ref/human/GRCh38/genomefile.5M.txt | parallel --delay 2 -j 10 "java -Xmx20g -jar $GATK_JAR -R ${genome_reference} -D ${dbSnp_reference} -T MuTect2 -stand_call_conf 30 -stand_emit_conf 10.0 -A FisherStrand -A QualByDepth -A VariantType -A DepthPerAlleleBySample -A HaplotypeScore -A AlleleBalance -I:tumor ${tumor}.final.bam -I:normal ${normal}.final.bam --cosmic ${cosmic} -o ${tumor}.{}.mutect.vcf -L {}"
     vcf-concat ${tumor}*.vcf | vcf-sort | vcf-annotate -n --fill-type | java -jar $SNPEFF_HOME/SnpSift.jar filter -p '((FS <= 60) & GEN[*].DP >= 10)' | perl -pe 's/TUMOR/'${tumor}'/' | perl -pe 's/NORMAL/'${normal}'/g' |bgzip > ${tumor}_${normal}.mutect.vcf.gz
 fi