Evidence map›Paper›PMID 36335497›Full record

ArticleMethods in molecular biology (Clifton, N.J.)2023

HapCUT2: A Method for Phasing Genomes Using Experimental Sequence Data.

Vikas Bansal

Abstract read
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In one paragraph

Article in Methods in molecular biology (Clifton, N.J.), 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 6 papers.

0numbers the graph read from it
0cells of the map it votes in
6citing 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

6 citing papers in PubMed.

  1. Article
  2. Review
  3. Constellation illuminates rare disease genetics.medRxiv : the preprint server for health sciences · 2025
    Article
  4. Article
  5. Article
  6. 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

1 author.

Vikas BansalSchool of Medicine, University of California San Diego, La Jolla, CA, USA. vibansal@ucsd.edu.

Funding

Computational methods for variant calling and haplotyping using long-read sequencing technologiesR01HG010759 · NHGRI · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI BANSAL, VIKAS · 2020 to 2023
$1.5M
NHGRI NIH HHS R01 HG010759
6 · The paper itself

Abstract

Rapid advances in high-throughput DNA sequencing technologies have enabled variant discovery from whole-genome sequencing (WGS) datasets; however linking variants on a chromosome together into haplotypes, also known as haplotype phasing, remains difficult. Human genomes are diploid and haplotype phasing is crucial for the complete interpretation and analysis of genetic variation.Hapcut2 ( https://github.com/vibansal/HapCUT2 ) is an open-source software for phasing diploid genomes using sequence data generated using different sequencing technologies and experimental methods. In this article, we give an overview of the algorithm used by Hapcut2 and describe how to use Hapcut2 for haplotype phasing of individual genomes using different types of sequence data.

Indexed as

Genome, HumanPolymorphism, Single NucleotideAlgorithmsHaplotypesHigh-Throughput Nucleotide SequencingHumansSequence Analysis, DNAHaplotypeHaplotype assemblyLong readsNext-generation sequencingPhasingProximity-ligationVariants

Identifiers

PMID36335497

What OpenQuestion holds

Textmetadata
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.