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. 2021 Aug 13;22:224. doi: 10.1186/s13059-021-02447-3

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© The Author(s) 2021

Open AccessThis article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated in a credit line to the data.

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Fig. 1 — Genotyping benchmark (simulated data): repeat capture. a Repeat size distribution of genotyping results from Straglr (ST), tandem-genotypes (TG) and RepeatHMM (RH) compared against real sizes (Truth) in simulated samples. Each sample is composed of 17 heterozygous loci (Table 1) with a reference and expanded alleles. Violin plot of each tool (orange, right) is juxtaposed with violin plot of the real distribution (blue, left) in each of the nine samples with different expansion sizes. Horizontal lines within the violin plot indicate the actual repeat sizes (y-positions) and relative frequencies (widths) detected. Red lines indicate sizes classified (ST) or generated (Truth) as the expanded allele (A_H), green the reference (A_L) allele, and black unclassified. P_KS indicates the p value from a KS test comparing the tool’s estimated and truth repeat size distributions. b True-positive (TP), false-positive (FP), and false-negative (FN) histograms in each of the nine experiments. Classifications are separated for expanded (dark red) and reference (green) alleles in ST based on the reported genotypes. No classification is possible with RH as supporting read identities were not revealed. Numbers in RH just indicate the total number of Truths reads plus the difference detected; e.g., 305 + 6 indicate 311 reads in total were detected by RH, 6 more than the total truth