#VariantCalling
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gpbees.bsky.social
📄 Variant Calling in the Dark Genome: Benchmarking SNV Calls in the Flanks of Structural Variants

academic.oup.com/gpb/advance-...
#Genomics #VariantCalling #StructuralVariants #Bioinformatics #LongReadSequencing #HumanGenomics 6/6
Validate User
academic.oup.com
September 11, 2026 at 7:30 AM
ergabiodiv.bsky.social
💡 #KnowledgeHighlight | Course: Methods in genomic variant calling by @embl.org @training.ebi.embl.org
🧬 🖥️
www.ebi.ac.uk/training/eve...

Explore open-access training materials in the ERGA #KnowledgeHub ➡️ knowledge.erga-biodiversity.eu #variantcalling #genomics #bioinformatics
February 9, 2026 at 8:30 AM
molbioevol.bsky.social
New graph-based tool ska lo enables reference-free detection of SNPs, indels, and variant groups from pathogen WGS data. Benchmarking shows high sensitivity, including in regions with dense mutations.

Link: doi.org/10.1093/molb...

#NewPaperAlert #bioinformatics #variantcalling #genomics
Reference-free variant calling with local graph construction with ska lo (SKA)
Abstract. The study of genomic variants is increasingly important for public health surveillance of pathogens. Traditional variant calling methods from who
doi.org
April 10, 2025 at 5:36 PM
commsmed.nature.com
🚨 NEW RESEARCH! ⚕️ 🩺

Bollas et al. introduce VarRNA, a novel classifier of single nucleotide variants and insertions/deletions from tumor transcriptomes using RNA-seq data.

https://bit.ly/460PXmY
#RNAseq #VariantCalling
Variant calling from RNA-Seq data reveals allele-specific differential expression of pathogenic cancer variants - Communications Medicine
Bollas and Gaither et al. present a method to classify simple germline and somatic sequence variants called from tumor RNA sequencing data alone. This machine learning-based approach simplifies variant classification and illustrates the importance of RNA in cancer molecular profiling.
bit.ly
June 20, 2025 at 9:48 AM
pg-pi3gey.bsky.social
Ok so this #deepvariant caller update from #google is BIG.
github.com/google/deepv...

- 1.6x time reduction (40% increase ??)
- Pangenome integration
- New model and improvements over previously model

Excited to try this new update 🧬💻

#bioinformatics #wgs #ngs #variantcalling
Release DeepVariant 1.8.0 · google/deepvariant
In this release: Small model integration: Speed increased by ~1.7x (40% runtime reduction) for WGS, PacBio, and ONT by introduction of additional small model. The small model identifies easy-to-...
github.com
December 9, 2024 at 6:39 AM
botsocamerica.bsky.social
From #AppsPlantSci's upcoming #Polyploidy issue🌿

Variant calling in polyploids for population and quantitative genetics -- a review of challenges & solutions, by Alyssa Phillips

bsapubs.onlinelibrary.wiley.com/doi/full/10.... #variantcalling #botany #plantjoy
The graphic shows how read mapping and the called allele dosage in allo- and autopolyploids differ due to the structure of the reference genome. Reads (gray) are shown aligning the reference genome (black), with alleles for the focal variant in pink or yellow. (A) In an allotetraploid with two subgenomes (subgenome K in light gray and subgenome N in dark gray), reads are mapped to one haplotype of each parental subgenome, and diploid genotypes are called. (B) In an autotetraploid with no preferential pairing, all reads are mapped to a single haplotype. Here, reads are aligned to a haplotype carrying the yellow A allele at the focal variant.
July 19, 2024 at 3:38 PM
dnanexus.bsky.social
Combine both short- and long-read data in one workflow with Sentieon pangenome pipelines. Donald Freed & Theresa Wohlever will show attendees how to leverage the latest variant calling techniques: event.on24.com/wcc/r/508266...

#WGS #Genomics #VariantCalling
Live webinar: Improving WGS Variant Calling with Public Pangenomes and Combined Short- and Long-Read Hybrid Pipelines. Happing on October 23 at 8am PT/11am ET. Speakers: Theresa Wohlever, Sr. Bioinformatics Scientist, DNAnexus and Donald Freed, PhD, Sr. Bioinformatics Scientist, Sentieon.
October 17, 2025 at 4:06 PM
dnanexus.bsky.social
Remove reference bias & improve variant calling accuracy by combining both short- and long-read data. Learn how to leverage Sentieon pangenome pipelines from Donald Freed & Theresa Wohlever: event.on24.com/wcc/r/508266...

#WGS #Genomics #VariantCalling
Live webinar: Improving WGS Variant Calling with Public Pangenomes and Combined Short- and Long-Read Hybrid Pipelines. Happing on October 23 at 8am PT/11am ET. Speakers: Theresa Wohlever, Sr. Bioinformatics Scientist, DNAnexus and Donald Freed, PhD, Sr. Bioinformatics Scientist, Sentieon.
October 8, 2025 at 3:58 PM
jsantoyo.bsky.social
A Pangenomic Method for Establishing a Somatic Variant Detection Resource in HapMap Mixtures. #SomaticVariantDetection #VariantCalling #Pangenomics #Genomics #Bioinformatics @biorxiv-genomic.bsky.social
www.biorxiv.org/content/10.1...
October 21, 2025 at 10:30 AM
jsantoyo.bsky.social
Accurate somatic small variant discovery for multiple sequencing technologies with DeepSomatic. #SomaticVariants #ShortReads #LongReads #VariantCalling #Genomics #Bioinformatics #ToolsBenchmarking #ReferenceDatasets @natbiotech.nature.com 🧬 🖥️
www.nature.com/articles/s41...
October 17, 2025 at 9:15 AM
jsantoyo.bsky.social
Finding easy regions for short-read variant calling from pangenome data. #VariantCalling #HumanGenome #PangenomeData #Bioinformatics #Genomics @gigascience.bsky.social
academic.oup.com/gigascience/...
September 22, 2025 at 1:49 PM
jsantoyo.bsky.social
Learning-based parallel acceleration for HaplotypeCaller. #VariantCalling #HaplotypeCaller #GATK #Genomics #Bioinformatics #BMCbioinformatics 🧬 🖥️
bmcbioinformatics.biomedcentral.com/articles/10....
September 2, 2025 at 9:15 AM
jsantoyo.bsky.social
A scalable distributed pipeline for reference-free variants calling. #VariantCalling #ReferenceFreeCalling #Bioinformatics #Genomics #BMCgenomics 🖥️ 🧪
bmcgenomics.biomedcentral.com/articles/10....
A scalable distributed pipeline for reference-free variants calling - BMC Genomics
Background Precision medicine pipelines typically begin with variant calling to identify disease-related mutations for optimal treatment selection. Reference-free approaches assess variations in the…
bmcgenomics.biomedcentral.com
June 5, 2025 at 8:32 AM
jsantoyo.bsky.social
Wgatools: an ultrafast toolkit for manipulating whole genome alignments. #WholeGenomeAlignment #Genomics #LongReads #Sequencing #VariantCalling #DataStructure #Bioinformatics #Rus 🧬 🖥️
academic.oup.com/bioinformati...
Wgatools: an ultrafast toolkit for manipulating whole genome alignments
AbstractSummary. With the rapid development of long-read sequencing technologies, the era of individual complete genomes is approaching. We have developed
academic.oup.com
April 5, 2025 at 10:56 AM
jsantoyo.bsky.social
The Scalable Variant Call Representation: Enabling Genetic Analysis Beyond One Million Genomes. #VariantCalling #VCF #ScalableVariantCall #SVCR #Genomics #Bioinformaitcs 🧬 🖥️
academic.oup.com/bioinformati...
The Scalable Variant Call Representation: Enabling Genetic Analysis Beyond One Million Genomes
AbstractMotivation. The Variant Call Format (VCF) is widely used in genome sequencing but scales poorly. For instance, we estimate a 150,000 genome VCF wou
academic.oup.com
January 6, 2025 at 8:19 PM
jsantoyo.bsky.social
SurVIndel2: improving copy number variant calling from next-generation sequencing using hidden split reads. #CNV #VariantCalling #Genomics @naturecomms.bsky.social 🧬 🖥️
www.nature.com/articles/s41...
SurVIndel2: improving copy number variant calling from next-generation sequencing using hidden split reads - Nature Communications
Copy number variants (CNVs) are the most common structural variants in human genomes however detecting them using short read sequencing is challenging. Here the authors introduce a method that uses a ...
www.nature.com
December 20, 2024 at 10:32 PM
jsantoyo.bsky.social
A robust benchmark for detecting low-frequency variants in the HG002 Genome In A Bottle NIST reference material. #LowFrequencyVariants #SomaticMosaicism #SomaticVariants #VariantCalling #ReferenceMaterials #GiAB #Benchmarking #Genomics 🧬 🖥️ @biorxivpreprint.bsky.social
www.biorxiv.org/content/10.1...
Source: https://www.biorxiv.org/content/10.1101/2024.12.02.625685v1.full.pdf
December 11, 2024 at 8:35 PM
jsantoyo.bsky.social
Clair3-RNA: A deep learning-based small variant caller for long-read RNA sequencing data. #LongReadRNAseq #VariantCalling #DeepLearning #Sequencing #Bioinformatics 🧬 🖥️
www.biorxiv.org/content/10.1...
Clair3-RNA: A deep learning-based small variant caller for long-read RNA sequencing data
Variant calling using long-read RNA sequencing (lrRNA-seq) can be applied to diverse tasks, such as capturing full-length isoforms and gene expression profiling. It poses challenges, however, due to h...
www.biorxiv.org
November 20, 2024 at 1:04 PM
antobeck.bsky.social
@medrxivpreprint.bsky.social on early access data generated by Baylor College of Medicine scientists with Illumina Constellation Mapped Read Technology. #genomics #VariantCalling #DRAGEN #Constellation bit.ly/48wm3I3
November 25, 2025 at 6:00 AM
antobeck.bsky.social
Great work out of the #illumina Artificial Intelligence Labs pubklised in @science.org today. PromotorAI to help call variants in non-coding promoter regions of genes. #DRAGEN #GeneRegulation #VariantCalling #WES #WGS
gnovakovsky.bsky.social Gherman Novakovsky @gnovakovsky.bsky.social · May 29
Excited to share my first contribution here at Illumina! We developed PromoterAI, a deep neural network that accurately identifies non-coding promoter variants that disrupt gene expression.🧵 (1/)
May 30, 2025 at 3:55 AM
djosergenomics.github.io
🚀New Blog Post!

Just finished a training project on variant calling using zebrafish data from @uofglasgow.bsky.social study on fisheries selection (PRJNA630223)

Walked through the full pipeline: QC → alignment → variant calling → VEP annotation

#Genomics #Zebrafish #Bioinformatics #VariantCalling
Discovering Mutations in fisheries-induced Selection of Zebrafish
Zebrafish Variant Calling Training Project
djosergenomics.github.io
July 23, 2025 at 12:27 AM
plantgenomics.bsky.social
Systematic evaluation of de novo mutation calling tools using whole genome sequencing data
doi.org/10.1101/2024...

Comparison of read mapping and variant calling tools for the analysis of plant NGS data
doi.org/10.1101/2020...

#Genomics #VariantCalling
Systematic evaluation of de novo mutation calling tools using whole genome sequencing data
De novo mutations (DNMs) are genetic alterations that occur for the first time in an offspring. DNMs have been found to be a significant cause of severe developmental disorders. With the widespread us...
doi.org
June 27, 2025 at 4:50 AM
plantgenomics.bsky.social
Allele Specific Expression Quality Control Fills Critical Gap in Transcriptome Assisted Rare Variant Interpretation
doi.org/10.1101/2025...

NAVIP: Unraveling the Influence of Neighboring Small Sequence Variants on Functional Impact Prediction
doi.org/10.1101/596718

#Bioinformatics #VariantCalling
doi.org
June 12, 2025 at 10:08 PM
plantgenomics.bsky.social
Variant Set Distillation
doi.org/10.1101/2024...

Comparison of read mapping and variant calling tools for the analysis of plant NGS data
doi.org/10.1101/2020...

#Bioinformatics #NGS #VariantCalling
Variant Set Distillation
Allelic heterogeneity -- the presence of multiple causal variants at a given locus -- has been widely observed across human traits. Combining the association signals across these distinct causal varia...
doi.org
May 28, 2025 at 4:11 AM
plantgenomics.bsky.social
Accelerated, Accurate, Hybrid Short and Long Reads Alignment and Variant Calling
doi.org/10.1101/2025...

Comparison of read mapping and variant calling tools for the analysis of plant NGS data
doi.org/10.1101/2020...

#Genomics #VariantCalling
Accelerated, Accurate, Hybrid Short and Long Reads Alignment and Variant Calling
Background: Integrating short-read and long-read sequencing technologies has become a promising approach for achieving accurate and comprehensive genomic analysis. While short-read sequencing (Illumin...
doi.org
May 2, 2025 at 4:34 AM