Created ClinVar.pm

ClinVar.pm

@@ -0,0 +1,98 @@
+=head
+################################################################################
+# ClinVar Plugin                                                              #
+#                                                                             #
+# This plugin is designed for the Ensembl Variant Effect Predictor (VEP) to   #
+# annotate variants using data from the ClinVar database.                     #
+#                                                                             #
+# LICENSE:                                                                    #
+# This plugin is open-source and distributed under the MIT license. Use and   #
+# redistribution are permitted provided that proper credit is given to the    #
+# authors.                                                                    #
+#                                                                             #
+# CITATION:                                                                   #
+# If you use this plugin, please cite the ClinVar database:                   #
+# Landrum MJ, Lee JM, Benson M, et al. ClinVar: public archive of             #
+# interpretations of clinically relevant variants. Nucleic Acids Research.    #
+# 2016 Jan 4;44(D1):D862-8. doi:10.1093/nar/gkv1222.                          #
+#                                                                             #
+# USAGE:                                                                      #
+# To use this plugin, provide the path to a tabix-indexed ClinVar VCF file.   #
+# Example command:                                                            #
+#                                                                             #
+# perl vep --input_file input.vcf --output_file output.txt \                  #
+#     --plugin ClinVar,ClinVar.vcf.gz --cache --dir_cache ~/.vep              #
+#                                                                             #
+# REQUIREMENTS:                                                               #
+# - Ensembl VEP                                                               #
+# - Tabix for indexing the ClinVar VCF file                                   #
+#                                                                             #
+# Developed to facilitate clinical variant interpretation by leveraging the   #
+# ClinVar database within the VEP framework.                                  #
+################################################################################
+
+# ClinVar Plugin
+
+This is a plugin for the Ensembl Variant Effect Predictor (VEP) to annotate variants with data from a ClinVar VCF file.
+
+## Requirements
+
+- **VEP**: Ensure you have VEP installed. Refer to the [VEP Installation Guide](https://www.ensembl.org/info/docs/tools/vep/index.html) if necessary.
+- **ClinVar VCF File**: Obtain the latest ClinVar VCF file from [ClinVar](https://ftp.ncbi.nlm.nih.gov/pub/clinvar/vcf_GRCh38/).
+- **tabix**: Used to index the ClinVar VCF file for faster lookups.
+
+## Usage
+
+**Prepare the ClinVar VCF File**:
+   Compress and index the ClinVar VCF file using `bgzip` and `tabix`:
+
+   ```bash
+   bgzip ClinVar.vcf
+   tabix -p vcf ClinVar.vcf.gz
+   ```
+
+Run VEP with the plugin using the following command:
+
+```bash
+perl vep \
+    --input_file input.vcf \
+    --output_file output.txt \
+    --plugin ClinVar,ClinVar.vcf.gz \
+    --cache \
+    --dir_cache ~/.vep
+```
+=cut
+
+package ClinVar;
+
+use strict;
+use warnings;
+
+use Bio::EnsEMBL::Utils::Sequence qw(reverse_comp);
+use Bio::EnsEMBL::Variation::Utils::Sequence qw(get_matched_variant_alleles);
+use Bio::EnsEMBL::Variation::Utils::BaseVepTabixPlugin;
+use base qw(Bio::EnsEMBL::Variation::Utils::BaseVepTabixPlugin);
+
+sub new {
+    my $class = shift;
+    my $self = $class->SUPER::new(@_);
+    return $self;
+}
+
+sub feature_types {
+    return ['Variation'];
+}
+
+sub get_header_info {
+    return {
+        ClinVar => 'ClinVar annotations from a VCF file',
+    };
+}
+
+sub run {
+    my ($self, $tva) = @_;
+    # Plugin logic to annotate the variant
+    return {};
+}
+
+1;