haplotypes

I got better results with synthetic haplotypes generated by downsampling the true haplotypes with a Markov model (using the BWT-based approach).

The distribution of local haplotypes within each context window was similar to the full set of haplotypes, but the noise from rare combinations of variants was mostly gone.

Our results provide evidence for directional selection operating in two major complementary haplotypes in Africa and East Asia.

For some reason, boys are hormonally behind by about 4 years now, also with significant differences between haplotypes.

Other people were doing haplotype inference with Markov models based on similarly large sets of haplotypes.

These should show a relationship to roughly equivalent sites in Siberia, and therefore to closely related early haplotypes in Eurasia.

It's nice to not need to sequence genomes of both parents in order to resolve haplotypes.

We found that two major SLC30A9 variant combinations (haplotypes) that are extremely frequent in Africa and East Asia, respectively, are expressed differentially.

We were using pangenomes based on thousands of (human) haplotypes as reference genomes.

The lineages are important because although the differences between the sequences are small, they are distinct, and there are no known transitional haplotypes.

An ARG can be conceptualized as a series of trees, mapped to individual sites, over phased haplotypes (chromosomes) in a panel of genomes.

A pangenome is a complex graph model that weaves together hundreds or more genomes/haplotypes—usually of one species, but the idea can extend across species too, or even cells within one individual (think cancer pangenomes).

It's just a shorthand for "Human DNA haplotypes (AKA markers) that occur at significant frequencies among populations that identify today as Jewish".

From the Science article: "However, limitations of BAC cloning led to an underrepresentation of repetitive sequences, and the opportunistic assembly of BACs derived from multiple individuals resulted in a mosaic of haplotypes.

("The high extinction rate [...] Failed introductions of intermediate haplotypes are also possible.") The whole point of their epidemiological modeling is to disentangle the likelihood of this happening.

> How to "bootstrap" the process The easiest thing you can do is to calculate your HLA/MHC haplotypes and then infer the risk of many common infectious and autoimmune disorders.