Evidence map›Paper›PMID 38418970›Full record

ArticleBMC bioinformatics2024

kalis: a modern implementation of the Li & Stephens model for local ancestry inference in R.

Louis J M Aslett, Ryan R Christ

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in BMC bioinformatics, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 2 papers.

0numbers the graph read from it
0cells of the map it votes in
2citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

2 citing papers in PubMed.

  1. Article
  2. Article
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

2 authors.

Louis J M AslettDepartment of Mathematical Sciences, Durham University, Stockton Road, Durham, DH1 3LE, UK. louis.aslett@durham.ac.uk.
Ryan R ChristDepartment of Genetics, Yale School of Medicine, 333 Cedar Street, New Haven, CT, 06520, USA.

Funding

Supplement Proposal: Accelerated Genome Aggregation and Joint Variant Calling EffortUM1HG008853 · NHGRI · WASHINGTON UNIVERSITY · PI HALL, IRA M, MILBRANDT, JEFFREY D · 2016 to 2020
$76.2M
NHGRI Centers for Common Disease Genomics UM1-HG008853NHGRI NIH HHS UM1 HG008853
6 · The paper itself

Abstract

backgroundApproximating the recent phylogeny of N phased haplotypes at a set of variants along the genome is a core problem in modern population genomics and central to performing genome-wide screens for association, selection, introgression, and other signals. The Li & Stephens (LS) model provides a simple yet powerful hidden Markov model for inferring the recent ancestry at a given variant, represented as an

resultsWe provide a high-performance engine to make these posterior decodings readily accessible with minimal pre-processing via an easy to use package kalis, in the statistical programming language R. kalis enables investigators to rapidly resolve the ancestry at loci of interest and developers to build a range of variant-specific ancestral inference pipelines on top. kalis exploits both multi-core parallelism and modern CPU vector instruction sets to enable scaling to hundreds of thousands of genomes.

conclusionsThe resulting distance matrices accessible via kalis enable local ancestry, selection, and association studies in modern large scale genomic datasets.

Indexed as

GenomeGenomicsEthnicityGenetics, PopulationHaplotypesHumansMarkov ChainsGenomicsHidden Markov modelHigh performance computationLi & Stephens modelProbabilistic haplotype modelR package

Identifiers

PMID38418970
PMCPMC10900616

What OpenQuestion holds

Textmetadata
LicenceCC BY
Read underepoch 390

Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.