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 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. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at (10.1186/s13059-022-02666-2).