diff --git a/README.md b/README.md
index 68882fb..6ed64a3 100644
--- a/README.md
+++ b/README.md
@@ -77,11 +77,11 @@ Create temporary shell variables pointing to where we'll store VEP and its cache
     export VEP_PATH=~/vep
     export VEP_DATA=~/.vep
 
-Download the v82 release of VEP:
+Download the v83 release of VEP:
 
     mkdir $VEP_PATH $VEP_DATA; cd $VEP_PATH
-    curl -LO https://github.com/Ensembl/ensembl-tools/archive/release/82.tar.gz
-    tar -zxf 82.tar.gz --starting-file variant_effect_predictor --transform='s|.*/|./|g'
+    curl -LO https://github.com/Ensembl/ensembl-tools/archive/release/83.tar.gz
+    tar -zxf 83.tar.gz --starting-file variant_effect_predictor --transform='s|.*/|./|g'
 
 Add that path to `PERL5LIB`, and the htslib subfolder to `PATH` where `tabix` will be installed:
 
@@ -90,18 +90,19 @@ Add that path to `PERL5LIB`, and the htslib subfolder to `PATH` where `tabix` wi
 
 Download and unpack VEP's offline cache for GRCh37, GRCh38, and GRCm38:
 
-    rsync -zvh rsync://ftp.ensembl.org/ensembl/pub/release-82/variation/VEP/homo_sapiens_vep_82_GRCh{37,38}.tar.gz $VEP_DATA
-    rsync -zvh rsync://ftp.ensembl.org/ensembl/pub/release-82/variation/VEP/mus_musculus_vep_82_GRCm38.tar.gz $VEP_DATA
-    cat $VEP_DATA/*_vep_82_GRC{h37,h38,m38}.tar.gz | tar -izxf - -C $VEP_DATA
+    rsync -zvh rsync://ftp.ensembl.org/ensembl/pub/release-83/variation/VEP/homo_sapiens_vep_83_GRCh{37,38}.tar.gz $VEP_DATA
+    rsync -zvh rsync://ftp.ensembl.org/ensembl/pub/release-83/variation/VEP/mus_musculus_vep_83_GRCm38.tar.gz $VEP_DATA
+    cat $VEP_DATA/*_vep_83_GRC{h37,h38,m38}.tar.gz | tar -izxf - -C $VEP_DATA
 
 Install the Ensembl API, the reference FASTAs for GRCh37/GRCh38/GRCm38, and some neat VEP plugins:
 
-    perl INSTALL.pl --AUTO afp --SPECIES homo_sapiens,mus_musculus --ASSEMBLY GRCh38,GRCm38 --PLUGINS CADD,ExAC,dbNSFP,UpDownDistance --DESTDIR $VEP_PATH --CACHEDIR $VEP_DATA
     perl INSTALL.pl --AUTO afp --SPECIES homo_sapiens --ASSEMBLY GRCh37 --PLUGINS CADD,ExAC,dbNSFP,UpDownDistance --DESTDIR $VEP_PATH --CACHEDIR $VEP_DATA
+    perl INSTALL.pl --AUTO afp --SPECIES homo_sapiens --ASSEMBLY GRCh38 --PLUGINS CADD,ExAC,dbNSFP,UpDownDistance --DESTDIR $VEP_PATH --CACHEDIR $VEP_DATA
+    perl INSTALL.pl --AUTO afp --SPECIES mus_musculus --ASSEMBLY GRCm38 --PLUGINS CADD,UpDownDistance --DESTDIR $VEP_PATH --CACHEDIR $VEP_DATA
 
 Convert the offline cache for use with tabix, that significantly speeds up the lookup of known variants:
 
-    perl convert_cache.pl --species homo_sapiens,mus_musculus --version 82_GRCh37,82_GRCh38,82_GRCm38 --dir $VEP_DATA
+    perl convert_cache.pl --species homo_sapiens,mus_musculus --version 83_GRCh37,83_GRCh38,83_GRCm38 --dir $VEP_DATA
 
 Download and index a custom ExAC r0.3 VCF, that skips variants overlapping known somatic hotspots:
 
@@ -110,7 +111,7 @@ Download and index a custom ExAC r0.3 VCF, that skips variants overlapping known
 
 Test running VEP in offline mode with the ExAC plugin, on the provided sample GRCh37 VCF:
 
-    perl variant_effect_predictor.pl --species homo_sapiens --assembly GRCh37 --offline --no_progress --everything --shift_hgvs 1 --check_existing --check_alleles --total_length --allele_number --no_escape --xref_refseq --dir $VEP_DATA --fasta $VEP_DATA/homo_sapiens/82_GRCh37/Homo_sapiens.GRCh37.75.dna.primary_assembly.fa --plugin ExAC,$VEP_DATA/ExAC.r0.3.sites.minus_somatic.vcf.gz --input_file example_GRCh37.vcf --output_file example_GRCh37.vep.txt
+    perl variant_effect_predictor.pl --species homo_sapiens --assembly GRCh37 --offline --no_progress --everything --shift_hgvs 1 --check_existing --check_alleles --total_length --allele_number --no_escape --xref_refseq --dir $VEP_DATA --fasta $VEP_DATA/homo_sapiens/83_GRCh37/Homo_sapiens.GRCh37.75.dna.primary_assembly.fa.gz --plugin ExAC,$VEP_DATA/ExAC.r0.3.sites.minus_somatic.vcf.gz --input_file example_GRCh37.vcf --output_file example_GRCh37.vep.txt
 
 Authors
 -------
diff --git a/maf2maf.pl b/maf2maf.pl
index 3885f4f..95e4fd3 100644
--- a/maf2maf.pl
+++ b/maf2maf.pl
@@ -16,8 +16,8 @@
 my ( $tum_depth_col, $tum_rad_col, $tum_vad_col ) = qw( t_depth t_ref_count t_alt_count );
 my ( $nrm_depth_col, $nrm_rad_col, $nrm_vad_col ) = qw( n_depth n_ref_count n_alt_count );
 my ( $vep_path, $vep_data, $vep_forks, $ref_fasta ) = ( "$ENV{HOME}/vep", "$ENV{HOME}/.vep", 4,
-    "$ENV{HOME}/.vep/homo_sapiens/82_GRCh37/Homo_sapiens.GRCh37.75.dna.primary_assembly.fa.gz" );
-my ( $species, $ncbi_build, $maf_center, $min_hom_vaf ) = ( "homo_sapiens", "GRCh37", ".", 0.7 );
+    "$ENV{HOME}/.vep/homo_sapiens/83_GRCh37/Homo_sapiens.GRCh37.75.dna.primary_assembly.fa.gz" );
+my ( $species, $ncbi_build, $cache_version, $maf_center, $min_hom_vaf ) = ( "homo_sapiens", "GRCh37", "", ".", 0.7 );
 my $perl_bin = $Config{perlpath};
 
 # Columns that can be safely borrowed from the input MAF
@@ -68,6 +68,7 @@
     'vep-forks=s' => \$vep_forks,
     'species=s' => \$species,
     'ncbi-build=s' => \$ncbi_build,
+    'cache-version=s' => \$cache_version,
     'ref-fasta=s' => \$ref_fasta,
 ) or pod2usage( -verbose => 1, -input => \*DATA, -exitval => 2 );
 pod2usage( -verbose => 1, -input => \*DATA, -exitval => 0 ) if( $help );
@@ -111,10 +112,15 @@
     ( -s $ref_fasta ) or die "ERROR: Reference FASTA not found: $ref_fasta\n";
     
     # Contruct VEP command using some default options and run it
-    my $vep_cmd = "$perl_bin $vep_path/variant_effect_predictor.pl --species $species --assembly $ncbi_build --offline --no_progress --no_stats --sift b --ccds --uniprot --hgvs --symbol --numbers --domains --gene_phenotype --regulatory --canonical --protein --biotype --uniprot --tsl --pubmed --variant_class --shift_hgvs 1 --check_existing --check_alleles --check_ref --total_length --allele_number --no_escape --xref_refseq --failed 1 --vcf --minimal --flag_pick_allele --pick_order canonical,tsl,biotype,rank,ccds,length --dir $vep_data --fasta $ref_fasta --input_file $vcf_file --output_file $vep_anno";
-    $vep_cmd .= " --fork $vep_forks" if( $vep_forks > 1 ); # VEP barks if it's set to 1
+    my $vep_cmd = "$perl_bin $vep_path/variant_effect_predictor.pl --species $species --assembly $ncbi_build --offline --no_progress --no_stats --sift b --ccds --uniprot --hgvs --symbol --numbers --domains --gene_phenotype --canonical --protein --biotype --uniprot --tsl --pubmed --variant_class --shift_hgvs 1 --check_existing --check_alleles --check_ref --total_length --allele_number --no_escape --xref_refseq --failed 1 --vcf --minimal --flag_pick_allele --pick_order canonical,tsl,biotype,rank,ccds,length --dir $vep_data --fasta $ref_fasta --input_file $vcf_file --output_file $vep_anno";
+    # VEP barks if --fork is set to 1. So don't use this argument unless it's >1
+    $vep_cmd .= " --fork $vep_forks" if( $vep_forks > 1 );
+    # Add --cache-version only if the user specifically asked for a version
+    $vep_cmd .= " --cache_version $cache_version" if( $cache_version );
     # Add options that only work on human variants
     $vep_cmd .= " --polyphen b --gmaf --maf_1kg --maf_esp" if( $species eq "homo_sapiens" );
+    # Add options that work for most species, except a few
+    $vep_cmd .= " --regulatory" unless( $species eq "canis_familiaris" );
     # Add options that only work on human variants mapped to the GRCh37 reference genome
     $vep_cmd .= " --plugin ExAC,$vep_data/ExAC.r0.3.sites.minus_somatic.vcf.gz" if( $species eq "homo_sapiens" and $ncbi_build eq "GRCh37" );
 
@@ -351,7 +357,8 @@ =head1 OPTIONS
  --vep-forks      Number of forked processes to use when running VEP [4]
  --species        Ensembl-friendly name of species (e.g. mus_musculus for mouse) [homo_sapiens]
  --ncbi-build     NCBI reference assembly of variants MAF (e.g. GRCm38 for mouse) [GRCh37]
- --ref-fasta      Reference FASTA file [~/.vep/homo_sapiens/82_GRCh37/Homo_sapiens.GRCh37.75.dna.primary_assembly.fa.gz]
+ --cache-version  Version of offline cache to use with VEP (e.g. 75, 82, 83) [Default: Installed version]
+ --ref-fasta      Reference FASTA file [~/.vep/homo_sapiens/83_GRCh37/Homo_sapiens.GRCh37.75.dna.primary_assembly.fa.gz]
  --help           Print a brief help message and quit
  --man            Print the detailed manual
 
diff --git a/maf2vcf.pl b/maf2vcf.pl
index adbe967..5eedb25 100644
--- a/maf2vcf.pl
+++ b/maf2vcf.pl
@@ -9,7 +9,7 @@
 use Pod::Usage qw( pod2usage );
 
 # Set any default paths and constants
-my $ref_fasta = "$ENV{HOME}/.vep/homo_sapiens/82_GRCh37/Homo_sapiens.GRCh37.75.dna.primary_assembly.fa.gz";
+my $ref_fasta = "$ENV{HOME}/.vep/homo_sapiens/83_GRCh37/Homo_sapiens.GRCh37.75.dna.primary_assembly.fa.gz";
 my ( $tum_depth_col, $tum_rad_col, $tum_vad_col ) = qw( t_depth t_ref_count t_alt_count );
 my ( $nrm_depth_col, $nrm_rad_col, $nrm_vad_col ) = qw( n_depth n_ref_count n_alt_count );
 
@@ -263,7 +263,7 @@ =head1 OPTIONS
  --input-maf      Path to input file in MAF format
  --output-dir     Path to output directory where VCFs will be stored, one per TN-pair
  --output-vcf     Path to output multi-sample VCF containing all TN-pairs [<output-dir>/<input-maf-name>.vcf]
- --ref-fasta      Path to reference Fasta file [~/.vep/homo_sapiens/82_GRCh37/Homo_sapiens.GRCh37.75.dna.primary_assembly.fa.gz]
+ --ref-fasta      Path to reference Fasta file [~/.vep/homo_sapiens/83_GRCh37/Homo_sapiens.GRCh37.75.dna.primary_assembly.fa.gz]
  --per-tn-vcfs    Specify this to generate VCFs per-TN pair, in addition to the multi-sample VCF
  --tum-depth-col  Name of MAF column for read depth in tumor BAM [t_depth]
  --tum-rad-col    Name of MAF column for reference allele depth in tumor BAM [t_ref_count]
diff --git a/vcf2maf.pl b/vcf2maf.pl
index c009bac..6dd3773 100644
--- a/vcf2maf.pl
+++ b/vcf2maf.pl
@@ -11,8 +11,8 @@
 
 # Set any default paths and constants
 my ( $tumor_id, $normal_id ) = ( "TUMOR", "NORMAL" );
-my ( $vep_path, $vep_data, $vep_forks, $ref_fasta ) = ( "$ENV{HOME}/vep", "$ENV{HOME}/.vep", 4, "$ENV{HOME}/.vep/homo_sapiens/82_GRCh37/Homo_sapiens.GRCh37.75.dna.primary_assembly.fa.gz" );
-my ( $species, $ncbi_build, $maf_center, $min_hom_vaf ) = ( "homo_sapiens", "GRCh37", ".", 0.7 );
+my ( $vep_path, $vep_data, $vep_forks, $ref_fasta ) = ( "$ENV{HOME}/vep", "$ENV{HOME}/.vep", 4, "$ENV{HOME}/.vep/homo_sapiens/83_GRCh37/Homo_sapiens.GRCh37.75.dna.primary_assembly.fa.gz" );
+my ( $species, $ncbi_build, $cache_version, $maf_center, $min_hom_vaf ) = ( "homo_sapiens", "GRCh37", "", ".", 0.7 );
 my $perl_bin = $Config{perlpath};
 
 # Hash to convert 3-letter amino-acid codes to their 1-letter codes
@@ -222,10 +222,15 @@ sub GetBiotypePriority {
         ( -s $ref_fasta ) or die "ERROR: Reference FASTA not found: $ref_fasta\n";
 
         # Contruct VEP command using some default options and run it
-        my $vep_cmd = "$perl_bin $vep_path/variant_effect_predictor.pl --species $species --assembly $ncbi_build --offline --no_progress --no_stats --sift b --ccds --uniprot --hgvs --symbol --numbers --domains --gene_phenotype --regulatory --canonical --protein --biotype --uniprot --tsl --pubmed --variant_class --shift_hgvs 1 --check_existing --check_alleles --check_ref --total_length --allele_number --no_escape --xref_refseq --failed 1 --vcf --minimal --flag_pick_allele --pick_order canonical,tsl,biotype,rank,ccds,length --dir $vep_data --fasta $ref_fasta --input_file $input_vcf --output_file $output_vcf";
-        $vep_cmd .= " --fork $vep_forks" if( $vep_forks > 1 ); # VEP barks if it's set to 1
+        my $vep_cmd = "$perl_bin $vep_path/variant_effect_predictor.pl --species $species --assembly $ncbi_build --offline --no_progress --no_stats --sift b --ccds --uniprot --hgvs --symbol --numbers --domains --gene_phenotype --canonical --protein --biotype --uniprot --tsl --pubmed --variant_class --shift_hgvs 1 --check_existing --check_alleles --check_ref --total_length --allele_number --no_escape --xref_refseq --failed 1 --vcf --minimal --flag_pick_allele --pick_order canonical,tsl,biotype,rank,ccds,length --dir $vep_data --fasta $ref_fasta --input_file $input_vcf --output_file $output_vcf";
+        # VEP barks if --fork is set to 1. So don't use this argument unless it's >1
+        $vep_cmd .= " --fork $vep_forks" if( $vep_forks > 1 );
+        # Add --cache-version only if the user specifically asked for a version
+        $vep_cmd .= " --cache_version $cache_version" if( $cache_version );
         # Add options that only work on human variants
         $vep_cmd .= " --polyphen b --gmaf --maf_1kg --maf_esp" if( $species eq "homo_sapiens" );
+        # Add options that work for most species, except a few we know about
+        $vep_cmd .= " --regulatory" unless( $species eq "canis_familiaris" );
         # Add options that only work on human variants mapped to the GRCh37 reference genome
         $vep_cmd .= " --plugin ExAC,$vep_data/ExAC.r0.3.sites.minus_somatic.vcf.gz" if( $species eq "homo_sapiens" and $ncbi_build eq "GRCh37" );
 
@@ -694,9 +699,10 @@ =head1 OPTIONS
  --vep-path       Folder containing variant_effect_predictor.pl [~/vep]
  --vep-data       VEP's base cache/plugin directory [~/.vep]
  --vep-forks      Number of forked processes to use when running VEP [4]
- --ref-fasta      Reference FASTA file [~/.vep/homo_sapiens/82_GRCh37/Homo_sapiens.GRCh37.75.dna.primary_assembly.fa.gz]
+ --ref-fasta      Reference FASTA file [~/.vep/homo_sapiens/83_GRCh37/Homo_sapiens.GRCh37.75.dna.primary_assembly.fa.gz]
  --species        Ensembl-friendly name of species (e.g. mus_musculus for mouse) [homo_sapiens]
  --ncbi-build     NCBI reference assembly of variants MAF (e.g. GRCm38 for mouse) [GRCh37]
+ --cache-version  Version of offline cache to use with VEP (e.g. 75, 82, 83) [Default: Installed version]
  --maf-center     Variant calling center to report in MAF [.]
  --min-hom-vaf    If GT undefined in VCF, minimum allele fraction to call a variant homozygous [0.7]
  --help           Print a brief help message and quit