ArticlePloS one2019
Variant analysis pipeline for accurate detection of genomic variants from transcriptome sequencing data.
Article in PloS one, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.
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Who cites it
20 citing papers in PubMed.
- Pan-transcriptome analysis of diverse chickpea accessions reveals specific expression patterns and genetic variations associated with agronomic traits.Plant molecular biology · 2026Article
- RapidmSphere · 2025Article
- Comparative analysis of genotype imputation strategies for SNPs calling from RNA-seq.BMC genomics · 2025Article
- Refined variant calling pipeline on RNA-seq data of breast cancer cell lines without matched-normal samples.BMC research notes · 2025Article
- Article
- Genetic variants in androgenetic alopecia: insights from scalp RNA sequencing data.Archives of dermatological research · 2024Article
- Genotype prediction of 336,463 samples from public expression data.bioRxiv : the preprint server for biology · 2024Article
- Critical assessment of on-premise approaches to scalable genome analysis.BMC bioinformatics · 2023Article
- BBmix: a Bayesian beta-binomial mixture model for accurate genotyping from RNA-sequencing.Bioinformatics (Oxford, England) · 2023Article
- RNA-Seq-based discovery of genetic variants and allele-specific expression of two layer lines and broiler chicken.Evolutionary applications · 2023Article
- Article
- Spatial variation in gene expression of Tasmanian devil facial tumors despite minimal host transcriptomic response to infection.BMC genomics · 2021Article
- Whole-Transcriptome Analysis by RNA Sequencing for Genetic Diagnosis of Mendelian Skin Disorders in the Context of Consanguinity.Clinical chemistry · 2021Article
- A versatile workflow to integrate RNA-seq genomic and transcriptomic data into mechanistic models of signaling pathways.PLoS computational biology · 2021Article
- Proteoform Identification by Combining RNA-Seq and Top-Down Mass Spectrometry.Journal of proteome research · 2021Article
- RNA-Seq Data for Reliable SNP Detection and Genotype Calling: Interest for Coding Variant Characterization andFrontiers in genetics · 2021Article
- Article
- Genome-Wide Development and Validation of Cost-Effective KASP Marker Assays for Genetic Dissection of Heat Stress Tolerance in Maize.International journal of molecular sciences · 2020Article
- Identification of SNPs and InDels associated with berry size in table grapes integrating genetic and transcriptomic approaches.BMC plant biology · 2020Article
- RASflow: an RNA-Seq analysis workflow with Snakemake.BMC bioinformatics · 2020Article
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Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The wealth of information deliverable from transcriptome sequencing (RNA-seq) is significant, however current applications for variant detection still remain a challenge due to the complexity of the transcriptome. Given the ability of RNA-seq to reveal active regions of the genome, detection of RNA-seq SNPs can prove valuable in understanding the phenotypic diversity between populations. Thus, we present a novel computational workflow named VAP (Variant Analysis Pipeline) that takes advantage of multiple RNA-seq splice aware aligners to call SNPs in non-human models using RNA-seq data only. We applied VAP to RNA-seq from a highly inbred chicken line and achieved high accuracy when compared with the matching whole genome sequencing (WGS) data. Over 65% of WGS coding variants were identified from RNA-seq. Further, our results discovered SNPs resulting from post transcriptional modifications, such as RNA editing, which may reveal potentially functional variation that would have otherwise been missed in genomic data. Even with the limitation in detecting variants in expressed regions only, our method proves to be a reliable alternative for SNP identification using RNA-seq data. The source code and user manuals are available at https://modupeore.github.io/VAP/.
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