Figure - PMC

Skip to main content

An official website of the United States government

Here's how you know

Here's how you know

Official websites use .gov
A .gov website belongs to an official government organization in the United States.

Secure .gov websites use HTTPS
A lock ( ) or https:// means you've safely connected to the .gov website. Share sensitive information only on official, secure websites.

View full-text article in PMC

. 2021 Sep 6;22:259. doi: 10.1186/s13059-021-02474-0

Search in PMC
Search in PubMed
View in NLM Catalog
Add to search

© The Author(s) 2021

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 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.

PMC Copyright notice

Fig. 9 — Nested genotyping procedure. Nodes with numbers mark the start and end of variant sites. In each panel, blue-filled nodes mark which site is being processed, red-filled nodes mark called alleles, and red paths mark alleles considered for genotyping. Ref is the reference allele, Alts are the alleles considered for genotyping, and GT is the called genotype. The example shows haploid genotyping. a Genotyping of child site 2. Allele “G” gets called. b Genotyping of child site 3. Allele “CC” gets called. c Genotyping of parent site 1. Alts are generated from the alleles called in child sites 2 and 3: allele “G” is used from site 2, and allele “CC” is used from site 3, producing alleles “AGT” and “CC”. Allele “AGT” gets called, going through site 2. d In c, the path going through site 2 was called. Because genotyping is haploid, the call at site 3 is invalidated (GT becomes “null”)