diff --git a/alignment/hisat_genotype.sh b/alignment/hisat_genotype.sh
index 6e225ebcf6f4ceebecc3a15982d70dc9ef4e9dd1..7e0655ecd393c73483cb63201d266c3c554b687c 100644
--- a/alignment/hisat_genotype.sh
+++ b/alignment/hisat_genotype.sh
@@ -11,10 +11,9 @@ usage() {
   exit 1
 }
 OPTIND=1 # Reset OPTIND
-while getopts :r:x:y:p:uh opt
+while getopts :x:y:p:uh opt
 do
     case $opt in
-        r) index_path=$OPTARG;;
         x) fq1=$OPTARG;;
         y) fq2=$OPTARG;;
 	u) umi='umi';;
@@ -26,7 +25,7 @@ done
 shift $(($OPTIND -1))
 
 # Check for mandatory options
-if [[ -z $pair_id ]] || [[ -z $index_path ]]; then
+if [[ -z $pair_id ]]; then
     usage
 fi
 
@@ -42,9 +41,9 @@ diff $fq1 $fq2 > difffile
 
 if [ -s difffile ]
 then
-hisatgenotype_extract_reads.py  -p 16  --database-list hla --base /project/shared/bicf_workflow_ref/hisat_genotype_hla/genotype_genome -1 $fq1 -2 $fq2 --out-dir hisatgeno_out
+hisatgenotype_extract_reads.py  -p 16  --database-list hla --base /project/shared/bicf_workflow_ref/human/hisat_genotype_hla/genotype_genome -1 $fq1 -2 $fq2 --out-dir hisatgeno_out
 else
-hisatgenotype_extract_reads.py  -p 16  --database-list hla --base /project/shared/bicf_workflow_ref/hisat_genotype_hla/genotype_genome -U $fq1 --out-dir hisatgeno_out
+hisatgenotype_extract_reads.py  -p 16  --database-list hla --base /project/shared/bicf_workflow_ref/human/hisat_genotype_hla/genotype_genome -U $fq1 --out-dir hisatgeno_out
 fi
 hisatgenotype_locus_samples.py -p 16 --region-list hla.A,hla.B,hla.C,hla.DQA1,hla.DQB1,hla.DRB1,hla.DPB1 --assembly --read-dir hisatgeno_out --out-dir ${pair_id}.hisat_hla > ${pair_id}.hisat_hla.txt
 
diff --git a/variants/annotvcf.sh b/variants/annotvcf.sh
index d3225209671997321d6a36d9befaa29fd842ed21..1f4d9720de5b41baf5b9b4dd3adaa0e807015c74 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,HG19_VARIANT,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,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/svcalling.sh b/variants/svcalling.sh
index 17bc77001347e37a528075d1f4da81ba0acf28c4..512fea26b84120c6c152a7de4b6fca04cadf5611 100755
--- a/variants/svcalling.sh
+++ b/variants/svcalling.sh
@@ -11,7 +11,7 @@ usage() {
   exit 1
 }
 OPTIND=1 # Reset OPTIND
-while getopts :r:p:b:i:e:n:a:h opt
+while getopts :r:p:b:i:n:a:h opt
 do
     case $opt in
         r) index_path=$OPTARG;;