Genome wide assembly-based structural variant calling

Abstract

This disclosure describes systems, non-transitory computer readable media, and methods for implementation of SV calling pipelines that can generate high-confidence diploid assemblies and SV call sets based on trio read data. For instance, a system is provided for implementing an SV calling pipeline via a bioinformatics subsystem executed on one or more processors that can receive a trio dataset of diploid read data of sequenced child (CH) and parental (M, P) genomes, and generate, based on consensus regions of the trio read data, a validated diploid assembly of the CH genome. Validation can be determined based on composition vectors of corresponding child and transmitting parent sequences at a given interval for each consensus region. The bioinformatics subsystem can then detect structural variants (SV) within the CH diploid assembly and output a VCF file of detected SVs as an SV truthset.

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