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. 2019 Apr 25;35(22):4716–4723. doi: 10.1093/bioinformatics/btz275

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© The Author(s) 2019. Published by Oxford University Press.

This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.

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Fig. 3. — (A) Comparison of different tools for variants discovery from reads taken from real WGS data of the Hapmap human individual NA12878. Results are discriminated by region type (single copy or repetitive), variant type (SNVs, Indels and STRs) and genotype in the PlatGen gold standard (homozygous or heterozygous). The proportion of FPPM is used as a measure of specificity. Curves are obtained varying the filter of minimum genotype quality (GQ field in the VCF file) from 0 to 90. (B) Runtime in minutes taken by the six tools to analyze the evaluated human samples. WGS, WES1 and WES2 correspond to one WGS and two WES datasets taken from the human Hapmap individual NA12878. SynDip corresponds to the synthetic diploid individual developed by Li et al. (2018)