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. 2020 Sep 22;11:4794. doi: 10.1038/s41467-020-18564-9

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© This is a U.S. government work and not under copyright protection in the U.S.; foreign copyright protection may apply 2020

Open Access This 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 license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license 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 license, visit http://creativecommons.org/licenses/by/4.0/.

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Fig. 1 — a We regenotyped DeepVariant (DV) heterozygous SNVs with WhatsHap using Oxford Nanopore Technologies (ONT) and PacBio HiFi (CCS) reads to find a confident set of SNVs with concordant genotypes from DV/CCS, WhatsHap/ONT, and WhatsHap/CCS—our Confident HETs for phasing. We selected 10x Genomics (10X) variants with phased blocks from the 10X VCF. For phasing, we used WhatsHap to combine phased blocks from 10X with ONT reads to get a single phased block across the MHC. b We binned PacBio HiFi reads into two haplotypes, which are denoted as orange and blue reads, using WhatsHap. c We performed diploid assembly using the Peregrine Assembler with the haplotype-binned HiFi reads. d We generated the benchmark variant callset from the assembled haplotigs using dipcall, and defined benchmark regions excluding SVs, exceptionally divergent regions, low-quality regions in the assembly, and long homopolymers.