MARS: a tool for haplotype-resolved population-based structural variation detection
biorxiv(2021)
摘要
Motivation Linked-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.
Results We 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.
Availability Source code and documentation are available on .
Contact maizie.zhou{at}vanderbilt.edu
Supplementary information Supplementary data are available at Bioinformatics online.
### Competing Interest Statement
The authors have declared no competing interest.
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关键词
structural variation detection,mars,haplotype-resolved,population-based
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