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

ABSTRACT: 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.

SUBMITTER: Yang J

PROVIDER: S-EPMC9077962 | biostudies-literature | 2022 May

REPOSITORIES: biostudies-literature

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

Yang Jianzhi J Chaisson Mark J P MJP

Genome biology 20220506 1

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 d ...[more]

PMID: 35524317

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