Script Version Requirements

In order for you to run the pipeline in its original script version, the following programs have to be in the path:

• liftOver
• MONSTER
• bgzip/tabix
• bedtools

The following items should be available:

• bigWigTools
• Linsight genome-wide scores
• CADD genome-wide scores
• Eigen scores computed genome-wide (The downloaded Eigen scores have to be processed... see details below)
• linked features file (preparation of the file is detailed below.)

The filtering of variants partially based on the annotation found in the vcf files. The following INFO fields have to be present:

• lof - loftee loss-of-function annotation (HC and LC for the high confidence and low confidence variants respectively)
• AN, AC and AF for filtering for allele frequency and missingness.