#VariantCalling

4 months ago

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...

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DNAnexus, Inc.

@dnanexus.bsky.social

4 months ago

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.

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

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4 months ago

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...

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5 months ago

Finding easy regions for short-read variant calling from pangenome data. #VariantCalling #HumanGenome #PangenomeData #Bioinformatics #Genomics @gigascience.bsky.social
academic.oup.com/gigascience/...

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@puckerlabpapers.bsky.social

6 months ago

Learning-based parallel acceleration for HaplotypeCaller. #VariantCalling #HaplotypeCaller #GATK #Genomics #Bioinformatics #BMCbioinformatics 🧬 🖥️
bmcbioinformatics.biomedcentral.com/articles/10....

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PuckerLab publications

7 months ago

NAVIP: Unraveling the influence of neighboring small sequence variants on functional impact prediction Once a suitable reference sequence has been generated, intra-species variation is often assessed by re-sequencing. Variant calling processes can reveal all differences between strains, accessions, gen...

NAVIP: Unraveling the Influence of Neighboring Small Sequence Variants on Functional Impact Prediction
doi.org/10.1371/jour...

#Bioinformatics #VariantCalling #VariantAnnotation #FunctionalGenomics #Genomics #PlantSci #DataScience #OpenData #OpenAccess #BigData #Python #100DaysOfCode

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Djoser Genomics

@djosergenomics.github.io

7 months ago

Discovering Mutations in fisheries-induced Selection of Zebrafish Zebrafish Variant Calling Training Project

🚀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

5 1 0 0

flalom

@flalom.bsky.social

7 months ago

🧬 Just released vcf-reformatter: A fast Rust tool for flattening VCF files with VEP annotations into TSV format! Ready to work with R/Py
Github: github.com/flalom/vcf-r...
- 🐛 Found a bug? github.com/flalom/vcf-r...
#bioinformatics #rust #vcf #genomics #opensource #variantcalling #cancer_research

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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...

8 months ago

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

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Communications Medicine

@commsmed.nature.com

8 months ago

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.

🚨 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

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@dnarnaresearch.bsky.social

9 months ago

Pangenome-aware DeepVariant Population-scale genomics information provides valuable prior knowledge for various genomic analyses, especially variant calling. A notable example of such application is the human pangenome reference...

Pangenome-aware DeepVariant
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...

#VariantCalling #Pangenomics #Bioinformatics

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9 months ago

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

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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…

9 months ago

A scalable distributed pipeline for reference-free variants calling. #VariantCalling #ReferenceFreeCalling #Bioinformatics #Genomics #BMCgenomics 🖥️ 🧪
bmcgenomics.biomedcentral.com/articles/10....

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Anthony Beckhouse

@antobeck.bsky.social

9 months ago

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

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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...

9 months ago

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

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ecSeq Bioinformatics

@ecseq.bsky.social

9 months ago

FINAL CALL - 9th Berlin Summer School in NGS Data Analysis 2025 (June 30 - July 4 in Berlin, Germany) - Apply Now 🌐 www.ecseq.com/summer-school

#NGS #BerlinSummerSchool #VariantCalling #Transcriptomics #RNAseq #DNAseq

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Medhat Mahmoud

@medhat.bsky.social

10 months ago

5/ Big thanks to @sedlazeck.bsky.social and Daniel Agustinho for their support and insight on this work!

Would love to hear your thoughts, feedback, or what tools you are using in your long-read work. 👇

#Genomics #Bioinformatics #PacBio #Nanopore #VariantCalling #GenomeAssembly #T2T #Epigenetics

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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...

10 months ago

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

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Complex structural variant visualization with SVTopo Structural variants are genomic variants that impact at least 50 nucleotides and can play major roles in diversity and human health. Many structural variants are complex multi-breakpoint rearrangement...

10 months ago

Complex structural variant visualization with SVTopo
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 #DataAnalysis

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Molecular Biology and Evolution

@molbioevol.bsky.social

11 months ago

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

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

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NAVIP: Unraveling the Influence of Neighboring Small Sequence Variants on Functional Impact Prediction Once a suitable reference sequence has been generated, intraspecific variation is often assessed by re-sequencing. Variant calling processes can reveal all differences between strains, accessions, gen...

11 months ago

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

Pervasive ancestry bias in variant effect predictors
doi.org/10.1101/2024...

#VariantCalling #Bioinformatics

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