ArticleBMC research notes2015
Fastq2vcf: a concise and transparent pipeline for whole-exome sequencing data analyses.
Article in BMC research notes, 2015. 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
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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
12 citing papers in PubMed.
- A Comprehensive Integrated Pipeline for Detection and Annotation of Variants in Whole Exome Sequencing Data.Molecular biotechnology · 2026Article
- GATES: A Lightweight Tool Automating Pathogenic Variant Discovery From Raw Whole-Exome Sequencing Data.Cancer informatics · 2026Article
- Whole-genome re-sequencing of the Baikal seal and other phocid seals for a glimpse into their genetic diversity, demographic history, and phylogeny.GigaByte (Hong Kong, China) · 2024Article
- Resources and tools for rare disease variant interpretation.Frontiers in molecular biosciences · 2023Review
- JWES: a new pipeline for whole genome/exome sequence data processing, management, and gene-variant discovery, annotation, prediction, and genotyping.FEBS open bio · 2021Article
- iWhale: a computational pipeline based on Docker and SCons for detection and annotation of somatic variants in cancer WES data.Briefings in bioinformatics · 2021Article
- Article
- DIVIS: Integrated and Customizable Pipeline for Cancer Genome Sequencing Analysis and Interpretation.Frontiers in oncology · 2021Article
- Review
- IMPACT: a whole-exome sequencing analysis pipeline for integrating molecular profiles with actionable therapeutics in clinical samples.Journal of the American Medical Informatics Association : JAMIA · 2016Article
- VDAP-GUI: a user-friendly pipeline for variant discovery and annotation of raw next-generation sequencing data.3 Biotech · 2016Article
- A Survey of Computational Tools to Analyze and Interpret Whole Exome Sequencing Data.International journal of genomics · 2016Review
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
3 authors.
Funding
Abstract
backgroundWhole-exome sequencing (WES) is a popular next-generation sequencing technology used by numerous laboratories with various levels of statistical and analytical expertise. Centralized databases, such as the Sequence Read Archive and the European Nucleotide Archive, allow data to be reanalyzed by independent labs to confirm results and derive additional insights. Access to new and shared data highlights the necessity for software that both lowers the statistical and analytical expertise required to generate results and promotes reproducible methodology among laboratories.
findingsWe have developed fastq2vcf, a pipeline that automates the genomic variant calling process using multiple callers. Fastq2vcf offers improved flexibility, efficiency, and reproducibility by seamlessly integrating several leading sequencing analysis tools. It outputs not only the annotated variant call set for each caller, but also the consensus variant call set shared by different callers. Furthermore, it can be customized and extended easily.
conclusionsOur software tool automatically generates executable command lines for a variety of tools required for analyzing WES data. It is also highly configurable and provides users with complete control of the processing procedure, making it easy to submit and track jobs in both single workstation and parallelized computing environments. By using this pipeline, WES analysis can be easily reproduced.
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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.