Extended Data Fig. 10: Quality assessment of variant calling.

In silico benchmarking and validation. a, Benchmarking of individual SV discovery tools and combined tools (“Merged”) for the sample HG002 evaluated against the Genome in a Bottle v0.6 Tier 1 using truvari. “Merged” strategy was defined by the best F1-score after testing all possible combinations of tools (for insertions and deletions separately). The same merging criteria was applied for all samples in AMP-AD. b, Benchmarking results of all 1,760 AMP-AD samples evaluated against the Genome in a Bottle v0.6 Tier 1 using truvari. In the box plots, the median values are shown in the central line, the box spans the first to the third quartiles and the whiskers extend 1.5 times the IQR from the box.