Our toolchain, which consists of additions to the VG toolkit and a standalone tool, RPVG, can construct spliced pangenome graphs, map RNA sequencing data to these graphs, and perform haplotype-aware expression quantification of transcripts in a pantranscriptome. We show that this workflow improves...
Haplotype-aware Hidden Markov Model for RNA (HaHMMR) is a method for detecting copy number variations (CNVs) from bulk RNA-seq data. Extending the haplotype-aware HMM in Numbat for single-cell RNA-seq, HaHMMR offers enhanced capabilities for detecting low-clonality CNVs from bulk data. This ...
Here, we introduce a haplotype-aware variant calling pipeline, PEPPER-Margin-DeepVariant, that produces state-of-the-art variant calling results with nanopore data. We show that our nanopore-based method outperforms the short-read-based single-nucleotide-variant identification method at the whole-...
To be clear, this issue is not widely discussed, so it would be nice if the Sarek team could look into it and possibly add some support for this kind of analysis. Describe the solution you'd like Add haplotype aware effect prediction. Possible tool chains: vcf+bam -> Whatshap (phasing)...
Haplotype-aware modeling of cis-regulatory effects highlights the gaps remaining in eQTL datadoi:10.1038/s41467-024-44710-8Expression Quantitative Trait Loci (eQTLs) are critical to understanding the mechanisms underlying disease-associated genomic loci. Nearly all protein-coding genes in the human ...
Haplotype-aware single-cell multiomics uncovers functional effects of somatic structural variationSomatic structural variants (SVs) are widespread in cancer genomes, however, their impact on tumorigenesis and intra-tumour heterogeneity is incompletely understood, since methods to functionally characterize the ...
Our novel toolchain can construct spliced pangenome graphs, map RNA-seq data to these graphs, and perform haplotype-aware expression quantification of transcripts in a pantranscriptome. This workflow improves accuracy over state-of-the-art RNA-seq mapping methods, and it can efficiently quantify ...
A Bayesian approach to haplotype-aware de novo genome assembly for polyploid organismsCapturing all genetic variation within a polyploid organism is a challenge. Most current de novo assemblers have no notion of the concept "ploidy". Consequently, when assembling the genome of diploid...
GBSmode: a pipeline for haplotype-aware analysis of genotyping-by-sequencing datadoi:10.1101/2021.09.20.461130Steven YatesBruno StuderCold Spring Harbor Laboratory
Motivated by recent works that model genetic variation in a geographic continuum, we propose a new spatial-aware haplotype copy model that jointly models geography and the haplotype copying process. We extend hidden Markov models of haplotype diversity such that at any given location, haplotypes that...