ArticleGenome biology2021
VariantStore: an index for large-scale genomic variant search.
Article in Genome biology, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 5 papers.
What it found
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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
5 citing papers in PubMed.
- LCPAN: efficient variation graph construction using locally consistent parsing.Genome biology · 2026Article
- Improving Hi-C contact matrices using genome graphs.bioRxiv : the preprint server for biology · 2023Article
- Advances in nanopore direct RNA sequencing.Nature methods · 2022Article
- The effect of genome graph expressiveness on the discrepancy between genome graph distance and string set distance.Bioinformatics (Oxford, England) · 2022Article
- VariantStore: an index for large-scale genomic variant search.Genome biology · 2021Article
Corrections and comments
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Authors and funding
3 authors.
Funding
Abstract
Efficiently scaling genomic variant search indexes to thousands of samples is computationally challenging due to the presence of multiple coordinate systems to avoid reference biases. We present VariantStore, a system that indexes genomic variants from multiple samples using a variation graph and enables variant queries across any sample-specific coordinate system. We show the scalability of VariantStore by indexing genomic variants from the TCGA project in 4 h and the 1000 Genomes project in 3 h. Querying for variants in a gene takes between 0.002 and 3 seconds using memory only 10% of the size of the full representation.
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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 OpenQuestion graph.