Article3 Biotech2016
VDAP-GUI: a user-friendly pipeline for variant discovery and annotation of raw next-generation sequencing data.
Article in 3 Biotech, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 9 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
9 citing papers in PubMed.
- Genome-wide pervasiveness and localized variation of [Formula: see text]-mer-based genomic signatures in eukaryotes.Scientific reports · 2026Article
- Variant Impact Predictor database (VIPdb), version 2: trends from three decades of genetic variant impact predictors.Human genomics · 2024Article
- Variant Impact Predictor database (VIPdb), version 2: Trends from 25 years of genetic variant impact predictors.bioRxiv : the preprint server for biology · 2024Article
- Whole Animal Genome Sequencing: user-friendly, rapid, containerized pipelines for processing, variant discovery, and annotation of short-read whole genome sequencing data.G3 (Bethesda, Md.) · 2023Article
- JWES: a new pipeline for whole genome/exome sequence data processing, management, and gene-variant discovery, annotation, prediction, and genotyping.FEBS open bio · 2021Article
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- Advancing Personalized Medicine Through the Application of Whole Exome Sequencing and Big Data Analytics.Frontiers in genetics · 2019Review
- VarGenius executes cohort-level DNA-seq variant calling and annotation and allows to manage the resulting data through a PostgreSQL database.BMC bioinformatics · 2018Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Even though next-generation sequencing (NGS) has become an invaluable tool in molecular biology, several laboratories with NGS facilities lack trained Bioinformaticians for data analysis. Here, focusing on the variant detection application of NGS analysis, we have developed a fully automated pipeline, namely Variant Discovery and Annotation Tool-Graphical User Interface (VDAP-GUI), which detects and annotates single nucleotide polymorphisms and insertions/deletions from raw sequence reads. VDAP-GUI consolidates several proven methods in each step such as quality control, trimming, mapping, variant detection and annotation. It supports multiple NGS platforms and has four methodological choices for variant detection. Further, it can re-analyze existing data with alternate thresholds and generates easily interpretable reports in html and tab-delimited formats. Using VDAP-GUI, we have analyzed a publically available human whole-exome sequence dataset. VDAP-GUI is developed using Perl/Tk programming, and is available for free download and use at http://sourceforge.net/projects/vdapgui/ .
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Identifiers
What OpenQuestion 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 OpenQuestion graph.