Fig. 1 | Nature Communications

Fig. 1

From: De novo and recessive forms of congenital heart disease have distinct genetic and phenotypic landscapes

Fig. 1The alternative text for this image may have been generated using AI.

Candidate gene discovery pipeline. PCGC trios were joint-genotyped with the Genome Analysis Tool Kit (GATK). Variant calls were annotated with the Ensembl Variant Effect Predictor (VEP version 90). Each trio VCF file was processed with the Variant Annotation, Analysis and Search Tool (VAAST version 3). Every candidate gene identified by VAAST in each trio was re-ranked with the Phenotype Driven Variant Ontological Re-ranking Tool (PHEVOR) using human phenotype ontology (HPO) terms matching the proband’s phenotype. To assess variant quality and remove potential false positives, each variant was adjudicated with the graph-based alignment tool, GRAPHITE. A final list of all recessive and de novo candidate genes was assembled for 2391 probands

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