de novo variant calling identifies cancer mutation signatures in the 1000 Genomes Project
Sign Up to like & getrecommendations! 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.
Sign Up to like & getrecommendations! 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.
Sign Up to like & getrecommendations! 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
Sign Up to like & getrecommendations! 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
Moss enables high sensitivity single-nucleotide variant calling from multiple bulk DNA tumor samples
Sign Up to like & getrecommendations! 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
Sign Up to like & getrecommendations! 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
Sign Up to like & getrecommendations! 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.
Sign Up to like & getrecommendations! 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
Clair3-trio: high-performance Nanopore long-read variant calling in family trios with trio-to-trio deep neural networks
Sign Up to like & getrecommendations! 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
Benchmarking the empirical accuracy of short-read sequencing across the M. tuberculosis genome
Sign Up to like & getrecommendations! Published in 2022 at "Bioinformatics"
DOI: 10.1093/bioinformatics/btac023
Abstract: MOTIVATION Short-read whole genome sequencing (WGS) is a vital tool for clinical applications and basic research. Genetic divergence from the reference genome, repetitive sequences, and sequencing bias reduce the performance of variant calling using short-read… read more here.
Keywords: short read; tuberculosis; genome; precision ... See more keywords
DeepSom: a CNN-based approach to somatic variant calling in WGS samples without a matched normal
Sign Up to like & getrecommendations! Published in 2023 at "Bioinformatics"
DOI: 10.1093/bioinformatics/btac828
Abstract: Abstract Motivation Somatic mutations are usually called by analyzing the DNA sequence of a tumor sample in conjunction with a matched normal. However, a matched normal is not always available, for instance, in retrospective analysis… read more here.
Keywords: somatic variant; wgs samples; deepsom; matched normal ... See more keywords