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   Articles with "variant calling" as a keyword



Variant calling in polyploids for population and quantitative genetics

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recommendations! Published in 2024 at "Applications in Plant Sciences"

DOI: 10.1002/aps3.11607

Abstract: Abstract Advancements in genome assembly and sequencing technology have made whole genome sequence (WGS) data and reference genomes accessible to study polyploid species. Compared to popular reduced‐representation sequencing approaches, the genome‐wide coverage and greater marker… read more here.

Keywords: genetics; wgs data; polyploid species; variant calling ... See more keywords

de novo variant calling identifies cancer mutation signatures in the 1000 Genomes Project

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recommendations! Published in 2022 at "Human Mutation"

DOI: 10.1002/humu.24455

Abstract: Detection of de novo variants (DNVs) is critical for studies of disease‐related variation and mutation rates. To accelerate DNV calling, we developed a graphics processing units‐based workflow. We applied our workflow to whole‐genome sequencing data… read more here.

Keywords: genomes project; cell; 1000 genomes; novo variant ... See more keywords

Importance of reliable variant calling and clear phenotyping when reporting on gene panel testing in renal disease.

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recommendations! Published in 2017 at "Kidney international"

DOI: 10.1016/j.kint.2017.07.009

Abstract: Genetic testing in kidney disease has been gaining more attention in recent years as an important diagnostic tool. Especially in selected cases, genetic testing can be a first mode of diagnostics in various renal diseases.… read more here.

Keywords: variant calling; disease; panel testing; gene ... See more keywords

HIVE-heptagon: A sensible variant-calling algorithm with post-alignment quality controls.

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recommendations! Published in 2017 at "Genomics"

DOI: 10.1016/j.ygeno.2017.01.002

Abstract: Advances in high-throughput sequencing (HTS) technologies have greatly increased the availability of genomic data and potential discovery of clinically significant genomic variants. However, numerous issues still exist with the analysis of these data, including data… read more here.

Keywords: alignment quality; variant calling; post alignment; post ... See more keywords

Functional equivalence of genome sequencing analysis pipelines enables harmonized variant calling across human genetics projects

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recommendations! Published in 2018 at "Nature Communications"

DOI: 10.1038/s41467-018-06159-4

Abstract: Hundreds of thousands of human whole genome sequencing (WGS) datasets will be generated over the next few years. These data are more valuable in aggregate: joint analysis of genomes from many sources increases sample size… read more here.

Keywords: variant calling; genetics; analysis; human genetics ... See more keywords
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Moss enables high sensitivity single-nucleotide variant calling from multiple bulk DNA tumor samples

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recommendations! Published in 2021 at "Nature Communications"

DOI: 10.1038/s41467-021-22466-9

Abstract: Intra-tumor heterogeneity renders the identification of somatic single-nucleotide variants (SNVs) a challenging problem. In particular, low-frequency SNVs are hard to distinguish from sequencing artifacts. While the increasing availability of multi-sample tumor DNA sequencing data holds… read more here.

Keywords: variant calling; dna; high sensitivity; single nucleotide ... See more keywords

Best practices for benchmarking germline small-variant calls in human genomes

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recommendations! Published in 2019 at "Nature Biotechnology"

DOI: 10.1038/s41587-019-0054-x

Abstract: Standardized benchmarking approaches are required to assess the accuracy of variants called from sequence data. Although variant-calling tools and the metrics used to assess their performance continue to improve, important challenges remain. Here, as part… read more here.

Keywords: variant calling; high confidence; variant calls; variant ... See more keywords

A synthetic-diploid benchmark for accurate variant calling evaluation

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recommendations! Published in 2018 at "Nature methods"

DOI: 10.1038/s41592-018-0054-7

Abstract: Existing benchmark datasets for use in evaluating variant-calling accuracy are constructed from a consensus of known short-variant callers, and they are thus biased toward easy regions that are accessible by these algorithms. We derived a… read more here.

Keywords: variant calling; benchmark; diploid benchmark; synthetic diploid ... See more keywords

Haplotype-aware variant calling with PEPPER-Margin-DeepVariant enables high accuracy in nanopore long-reads.

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recommendations! Published in 2021 at "Nature methods"

DOI: 10.1038/s41592-021-01299-w

Abstract: Long-read sequencing has the potential to transform variant detection by reaching currently difficult-to-map regions and routinely linking together adjacent variations to enable read-based phasing. Third-generation nanopore sequence data have demonstrated a long read length, but… read more here.

Keywords: variant calling; haplotype aware; pepper margin; margin deepvariant ... See more keywords

Empirical Bayes single nucleotide variant-calling for next-generation sequencing data

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recommendations! Published in 2024 at "Scientific Reports"

DOI: 10.1038/s41598-024-51958-z

Abstract: One of the fundamental computational problems in cancer genomics is the identification of single nucleotide variants (SNVs) from DNA sequencing data. Many statistical models and software implementations for SNV calling have been developed in the… read more here.

Keywords: bayes single; variant calling; single nucleotide; sequencing data ... See more keywords

Clair3-trio: high-performance Nanopore long-read variant calling in family trios with trio-to-trio deep neural networks

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recommendations! Published in 2022 at "Briefings in Bioinformatics"

DOI: 10.1093/bib/bbac301

Abstract: Accurate identification of genetic variants from family child-mother-father trio sequencing data is important in genomics. However, state-of-the-art approaches treat variant calling from trios as three independent tasks, which limits their calling accuracy for Nanopore long-read… read more here.

Keywords: family; nanopore long; clair3 trio; trio trio ... See more keywords