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.

Compatible Tools and Formats

While any variant annotation tool can be used, AlloPipe has been specifically developed and tested with .VCF v4.2 files annotated using VEP versions 103, 104, 110, and 111.

VEP Installation and Configuration

• Download cache files and FASTA files matching your genome reference to run VEP offline.
• Add VEP to your system PATH by editing your ~/.profile or ~/.bash_profile:

export PATH=%%PATH/TO/VEP%%:${PATH}

Annotation Command

Use the following command to annotate your .VCF file(s) with VEP. Adjust the parameters as needed:

vep --fork 4 --cache --assembly <GRChXX> --offline --af_gnomade \
-i <FILE-TO-ANNOTATE>.vcf -o <ANNOTATED-FILE>.vcf \
--coding_only --pick_allele --use_given_ref --vcf

Replace <GRChXX> with your genome version, and provide the appropriate input/output file paths.

Next Steps

Once your variant-annotated files are ready, proceed to launch your first AlloPipe run!