TT-Mars: structural variants assessment based on haplotype-resolved assemblies

Variant benchmarking is often performed by comparing a test callset to a gold standard set of variants. In repetitive regions of the genome, it may be difficult to establish what is the truth for a call, for example, when different alignment scoring metrics provide equally supported but different va...

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Bibliographic Details
Published in:Genome Biology 2022-05, Vol.23 (1), p.110-110, Article 110
Main Authors: Yang, Jianzhi, Chaisson, Mark J P
Format: Article
Language:English
Subjects:
Accuracy
Algorithms
Benchmarking
Consortia
Genome
Genomes
Haplotypes
High-Throughput Nucleotide Sequencing
Method
Methods
Polymorphism, Single Nucleotide
Software
Structural variants
Validation
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Summary:Variant benchmarking is often performed by comparing a test callset to a gold standard set of variants. In repetitive regions of the genome, it may be difficult to establish what is the truth for a call, for example, when different alignment scoring metrics provide equally supported but different variant calls on the same data. Here, we provide an alternative approach, TT-Mars, that takes advantage of the recent production of high-quality haplotype-resolved genome assemblies by providing false discovery rates for variant calls based on how well their call reflects the content of the assembly, rather than comparing calls themselves.
ISSN:1474-760X
1474-7596
1474-760X
DOI:10.1186/s13059-022-02666-2