Analysis Overview
Primary input files for the analysis of the genes include exome sequencing variant data in the form of variant call format (VCF) files for the myelomeningocele subject samples from Genome Analysis Toolkit (GATK) sequencing and VCF files for the reference population from version 2 of the Genome Aggregation Database (gnomAD) (Karczewski et al., 2019). Variant calls were filtered based on quality control metrics and annotated for genomic function before variant allele burden in the myelomeningocele cases was compared to that of a reference population (Fig 1). The steps of the analysis were largely performed using custom scripts written in Python 2.7 and R 3.5.3.