人类基因组的Phasing原理是什么？ - 知乎专栏
在开展大规模的基因组研究计划时（如Hapmap、国际千人基因组、Haplotype reference consortium以及各国家的国家基因组计划），通过构建基于隐马尔可夫模型（HMM）等的Phasing算法就可以依据测序数据或者芯片数据，反推出每个个体最有可能的单倍体，完 …
Haplotype estimation - Wikipedia
In genetics, haplotype estimation (also known as "phasing") refers to the process of statistical estimation of haplotypes from genotype data. The most common situation arises when genotypes are collected at a set of polymorphic sites from a group of individuals.
Eagle2单倍型定相工具 Haplotype phasing - 知乎 - 知乎专栏
如果只是想对chr X 的non-PAR部分进行phasing，那么只需输入 chrom 23 即可。 如果要对整个X染色体（包括PAR与non-PAR），那么需要首先将plink文件中PAR与non-PAR的基因型合并，（可以使用plink的-merge-x）。 VCF文件则不需要额外处理。 2.参考的遗传图谱. 如果你的PILNK文件没有相应的遗传坐标文件（单位为摩根），可以使用eagle提供的事先处理好的参考图谱（从HapMap下载并转换格式）。 使用时，选项如下： 3.缺失值处理. phasing过程中，缺失 …
HapCUT: an efficient and accurate algorithm for the haplotype …
2008年8月9日 · In this article, we consider the haplotype assembly problem in the most general setting, i.e. fragments of any length and with an arbitrary number of gaps. Results: We describe a novel combinatorial approach for the haplotype assembly problem based on computing max-cuts in certain graphs derived from the sequenced fragments.
Haplotype phasing: existing methods and new developments
2011年9月16日 · We assess the haplotype phasing methods that are available, focusing in particular on statistical methods, and we discuss the practical aspects of their application. We also describe recent...
Lecture 10: Haplotype Phasing - Community Recovery
2018年2月8日 · Haplotype Phasing. Haplotype phasing is the problem of inferring information about an individual’s haplotype. To solve this problem, there are many methods. First, we discuss what kind of data is needed to perform phasing. Let’s say we have two variants, SNP1 and SNP2.
Sequencing 101: ploidy, haplotypes, and phasing - PacBio
2020年12月10日 · Phasing involves separating maternally and paternally inherited copies of each chromosome into haplotypes to get a complete picture of genetic variation. Recent advances in DNA sequencing technology and the tools used to assemble and phase genomes allow large blocks of the sequence to be phased directly from DNA sequencing reads of one individual.
HaplotypeTools: a toolkit for accurately identifying …
2021年11月22日 · HaplotypeTools is a new toolset to phase variant sites using VCF and BAM files and to analyse phased VCFs. Phasing is achieved via the identification of reads overlapping ≥ 2 heterozygous positions and then extended by additional reads, a process that can be parallelized across a computer cluster.
Reference-based phasing using the Haplotype Reference
2016年10月3日 · We introduce a new phasing algorithm, Eagle2, that attains high accuracy across a broad range of cohort sizes by efficiently leveraging information from large external reference panels (such as...
Graphasing: phasing diploid genome assembly graphs with single …
2024年10月10日 · Here, we present Graphasing, a workflow which synthesizes the global phase signal of Strand-seq with assembly graph topology to produce chromosome-scale de novo haplotypes for diploid genomes. Graphasing readily integrates with any assembly workflow that both outputs an assembly graph and has a haplotype assembly mode.