diff --git a/variants/annotvcf.sh b/variants/annotvcf.sh
index f3d246289978d343b37ec7b4632e16021efb9b36..7bc785b9e608a0595fa454e065f809a4dca5a0b3 100755
--- a/variants/annotvcf.sh
+++ b/variants/annotvcf.sh
@@ -36,7 +36,7 @@ then
     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-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
+    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
     tabix ${pair_id}.annot.vcf.gz
 else 
     if [[ $index_path == '/project/shared/bicf_workflow_ref/GRCm38' ]]
diff --git a/variants/filter_cnvkit.pl b/variants/filter_cnvkit.pl
index 2f60eef3d84c6973f4568c831486e6a5f98c5e6b..b7504ad5823d209c647e3ae270f9e71df8f55f62 100755
--- a/variants/filter_cnvkit.pl
+++ b/variants/filter_cnvkit.pl
@@ -60,11 +60,19 @@ while (my $line = <CNR>) {
     my ($chr,$start,$end,$geneids,$log2,$depth,$weight) = split(/\t/,$line);
     my $key = $chr.":".$start."-".$end;
     my %genes;
-    my @ids = split(/;|,/,$geneids);
-    foreach my $gid (@ids) {
-	my ($key,$value) = split(/=/,$gid);
-	if ($key eq 'ensembl_gn' || $key eq 'identifier') {
-	    $genes{$value} = 1 if $keep{$value};
+    if ($geneids =~ m/ensembl_gn/g) {
+	my @ids = split(/;|,/,$geneids);
+	foreach my $gid (@ids) {
+	    my ($key,$value) = split(/=/,$gid);
+	    if ($key eq 'ensembl_gn' || $key eq 'identifier') {
+		$genes{$value} = 1 if $keep{$value};
+	    }
+	}
+    }else {
+	my @ids = split(/,/,$geneids);
+	foreach my $gid (@ids) {
+	    my ($gene,$trxid,$exonnum,$strand) = split(/\|/,$gid);
+	    $genes{$gene} = 1 if $keep{$gene};
 	}
     }
     foreach $gene (keys %genes) {
@@ -81,11 +89,19 @@ while (my $line = <IN>) {
     next if ($chr eq 'chrX' && $cn == 1);
     my $key = $chr.":".$start."-".$end;
     my %genes;
-    my @ids = split(/;|,/,$geneids);
-    foreach my $gid (@ids) {
-	my ($key,$value) = split(/=/,$gid);
-	if ($key eq 'ensembl_gn' || $key eq 'identifier') {
-	    $genes{$value} = 1 if $keep{$value};
+    if ($geneids =~ m/ensembl_gn/g) {
+	my @ids = split(/;|,/,$geneids);
+	foreach my $gid (@ids) {
+	    my ($key,$value) = split(/=/,$gid);
+	    if ($key eq 'ensembl_gn' || $key eq 'identifier') {
+		$genes{$value} = 1 if $keep{$value};
+	    }
+	}
+    }else {
+	my @ids = split(/,/,$geneids);
+	foreach my $gid (@ids) {
+	    my ($gene,$trxid,$exonnum,$strand) = split(/\|/,$gid);
+	    $genes{$gene} = 1 if $keep{$gene};
 	}
     }
     my $len = sprintf("%.1f",($end-$start)/1000);