Input Requirements

AlloPipe requires input file(s) to be variant-annotated .VCF files. We strongly recommend using the latest version of VEP for variant annotation.
AlloPipe has been specifically developed and tested with .VCF v4.2 files annotated using VEP versions 103, 104, 110, and 111.

Annotation recommendations

We recommend to annotate your .VCF file(s) with the following parameters :

--af_gnomade --coding_only --pick_allele --use_given_ref --vcf