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.