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. 2022 Mar 21;28(3):513–516. doi: 10.1038/s41591-022-01735-0

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© The Author(s) 2022

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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Extended Data Fig. 7 — Each parent’s genome is phased using PS parental haplotypes (see Supplemental Note 1) and population reference panels using SHAPEIT4. The PS parental haplotypes serve as a scaffold (step 1) consisting of approximately 200,000 variants. WGS of both parents are provisionally phased using population reference panels and compared with PS Parental Haplotypes. Overlapping positions between the parental support haplotypes and provisionally phased WGS are marked as having concordant (1) or discordant (0) phase (step 2) and grouped into blocks (step 3). Interval regions between these blocks are suggestive of either meiotic recombination or error in phasing one or both parents; these sites are discarded (positions marked with ‘X’ in step 3). All remaining sites are used in subsequent assembly of the ‘Phased Parental Genome’ (step 4).