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bioRxiv · 10.1101/2021.09.27.462061

MARS: a tool for haplotype-resolved population-based structural variation detection

Zhang, L.·Sidow, A.·Zhou, X.
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Abstract

MotivationLinked-reads enables genome-wide phased diploid assemblies. These haplotype-resolved assemblies allow us to genotype structural variants (SVs) with a high sensitivity and be able to further phase them. Yet, existing SV callers are designed for haploid genome assemblies only, and there is no tool to call SV from a large population of diploid assemblies which can define and refine SVs from a global view. ResultsWe introduce MARS (Multiple Alignment-based Refinement of Svs) in linked-reads for the detection of the most common SV types - indels from diploid genome assemblies of a large population. We evaluated SVs from MARS based on Mendelian law of inheritance and PacBio HiFi reads and it achieved a high validation rate around 73%-87% for indels that we have selected from 34 assembled samples. AvailabilitySource code and documentation are available on https://github.com/maiziex/MARS. Contactmaizie.zhou@vanderbilt.edu Supplementary informationSupplementary data are available at Bioinformatics online.

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Zhang, L., Sidow, A., Zhou, X.. 2021-09-29. MARS: a tool for haplotype-resolved population-based structural variation detection. https://doi.org/10.1101/2021.09.27.462061

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