Tootfinder

Finding easy regions for short-read variant calling from pangenome data
Heng Li
https://arxiv.org/abs/2507.03718 https://arxiv.org/pd…

Finding easy regions for short-read variant calling from pangenome data
Background: While benchmarks on short-read variant calling suggest low error rate below 0.5%, they are only applicable to predefined confident regions. For a human sample without such regions, the error rate could be 10 times higher. Although multiple sets of easy regions have been identified to alleviate the issue, they fail to consider non-reference samples or are biased towards existing short-read data or aligners. Results: Here, using hundreds of high-quality human assemblies, we derived …