[ensembl-dev] variant effect predictor not reading through list of contigs?

[Mark Aquino]

Hey,

I'm having an issue getting the variant effect predictor to actually analyze my entire VCF file, for some reason it has been completely skipping entire chromosomes. notably, MT.

My VCF is in b37 format.

./variant_effect_predictor.pl -i kabuki.b37.vcf --sift b --polyphen b --condel b --format vcf -r ~/script_outputs/registry.txt  -w

-Mark Aquino