ArticleNature communications2021
PopDel identifies medium-size deletions simultaneously in tens of thousands of genomes.
Article in Nature communications, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.
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.
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.
Who cites it
12 citing papers in PubMed, 17 citations in OpenAlex.
- CNValidatron: accurate and efficient validation of PennCNV calls using computer vision.BMC bioinformatics · 2026Article
- CNValidatron: Accurate And Efficient Validation of PennCNV Calls Using Computer Vision.bioRxiv : the preprint server for biology · 2025Article
- Review
- Best practices for germline variant and DNA methylation analysis of second- and third-generation sequencing data.Human genomics · 2024Review
- GGTyper: genotyping complex structural variants using short-read sequencing data.Bioinformatics (Oxford, England) · 2024Article
- VISTA: an integrated framework for structural variant discovery.Briefings in bioinformatics · 2024Article
- Whole genome sequencing identifies structural variants contributing to hematologic traits in the NHLBI TOPMed program.Nature communications · 2022Article
- A comprehensive benchmarking of WGS-based deletion structural variant callers.Briefings in bioinformatics · 2022Article
- Large-Scale Screening for Monogenic and Clinically Defined Familial Hypercholesterolemia in Iceland.Arteriosclerosis, thrombosis, and vascular biology · 2021Article
- Novel sequencing technologies and bioinformatic tools for deciphering the non-coding genome.Medizinische Genetik : Mitteilungsblatt des Berufsverbandes Medizinische Genetik e.V · 2021Article
- PopDel identifies medium-size deletions simultaneously in tens of thousands of genomes.Nature communications · 2021Article
- Hi-C Identifies Complex Genomic Rearrangements and TAD-Shuffling in Developmental Diseases.American journal of human genetics · 2020Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
10 authors at 4 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Thousands of genomic structural variants (SVs) segregate in the human population and can impact phenotypic traits and diseases. Their identification in whole-genome sequence data of large cohorts is a major computational challenge. Most current approaches identify SVs in single genomes and afterwards merge the identified variants into a joint call set across many genomes. We describe the approach PopDel, which directly identifies deletions of about 500 to at least 10,000 bp in length in data of many genomes jointly, eliminating the need for subsequent variant merging. PopDel scales to tens of thousands of genomes as we demonstrate in evaluations on up to 49,962 genomes. We show that PopDel reliably reports common, rare and de novo deletions. On genomes with available high-confidence reference call sets PopDel shows excellent recall and precision. Genotype inheritance patterns in up to 6794 trios indicate that genotypes predicted by PopDel are more reliable than those of previous SV callers. Furthermore, PopDel's running time is competitive with the fastest tested previous tools. The demonstrated scalability and accuracy of PopDel enables routine scans for deletions in large-scale sequencing studies.
Indexed as
Identifiers
What Socratic holds
Registered trials
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 Socratic graph.