Input File Preparation

The main input file to the pVACseq pipeline is a VCF file. The VCF needs to contain sample genotype information (GT field). The VCF needs to be annotated with VEP to add transcript information.

If filtering on variant allele fractions (VAFs), depth, and expression values is desired, the VCF also needs to be annotated with this data.

Refer to the following sections for instructions on how to annotate your VCF with these data and how to produce a VCF for proximal variant analysis.

• Adding genotype sample information to your VCF
• Annotating your VCF with VEP
• Adding coverage data to your VCF
• Adding expression data to your VCF
• Creating a phased VCF of proximal variants