I want to annotate with SNP-proxys (r^2>0.8) for each variant in my VCF-file. For that, I am trying to use the plugin LD (https://github.com/Ensembl/VEP_plugins/blob/release/88/LD.pm) for VEP.
When running the VEP script (version 87) like this:
perl variant_effect_predictor.pl --species homo_sapiens --input_file input.vcf.gz --output_file output.vcf --cache --plugin LD,1000GENOMES:phase_3:EUR,0.8 --port 3337 --buffer_size 100000 --chr 1-22,X,Y --no_consequences
I can see following warning message in the output:
Warning: a connection to the database is required to calculate LD
Do i need to download a database prior running the script with this plugin cause I cannot see any annotations, and I have approximately 300 000 variants in my VCF, none of those were annotated with any SNP-proxys. For the VEP I use assembly 87_GRCh37 and cache file homo_sapiens_vep_87_GRCh37.tar.gz.