Results 11 to 20 of about 709,139 (287)
Multithreaded variant calling in elPrep 5. [PDF]
PLoS ONE, 2021 We present elPrep 5, which updates the elPrep framework for processing sequencing alignment/map files with variant calling. elPrep 5 can now execute the full pipeline described by the GATK Best Practices for variant calling, which consists of PCR and ...
Charlotte Herzeel +5 more
doaj +7 more sources
Changepoint Analysis for Efficient Variant Calling [PDF]
, 2014 We present CAGe, a statistical algorithm which exploits high sequence identity between sampled genomes and a reference assembly to streamline the variant calling process. Using a combination of changepoint detection, classification, and online variant detection, CAGe is able to call simple variants quickly and accurately on the 90-95% of a sampled ...
Adam E. Bloniarz +6 more
openaire +5 more sources
CoVaCS: a consensus variant calling system [PDF]
BMC Genomics, 2018 Background The advent and ongoing development of next generation sequencing technologies (NGS) has led to a rapid increase in the rate of human genome re-sequencing data, paving the way for personalized genomics and precision medicine. The body of genome
Matteo Chiara +9 more
doaj +6 more sources
Best practices for variant calling in clinical sequencing
Genome Medicine, 2020 Next-generation sequencing technologies have enabled a dramatic expansion of clinical genetic testing both for inherited conditions and diseases such as cancer.
Daniel C. Koboldt
doaj +3 more sources
Information theoretic alignment free variant calling [PDF]
PeerJ Computer Science, 2016 While traditional methods for calling variants across whole genome sequence data rely on alignment to an appropriate reference sequence, alternative techniques are needed when a suitable reference does not exist. We present a novel alignment and assembly
Justin Bedo +3 more
doaj +4 more sources
Halvade somatic: Somatic variant calling with Apache Spark [PDF]
GigaScience, 2022 Abstract Background The accurate detection of somatic variants from sequencing data is of key importance for cancer treatment and research. Somatic variant calling requires a high sequencing depth of the tumor sample, especially when the detection of low-frequency variants is also desired.
Dries Decap +7 more
openaire +5 more sources
Genome-wide variant calling in reanalysis of exome sequencing data uncovered a pathogenic TUBB3 variant [PDF]
, 2022 Almost half of all individuals affected by intellectual disability (ID) remain undiagnosed. In the Solve-RD project, exome sequencing (ES) datasets from unresolved individuals with (syndromic) ID (n = 1,472 probands) are systematically reanalyzed ...
Jackson, Adam +86 more
core +8 more sources
Variant calling: Considerations, practices, and developments [PDF]
Human Mutation, 2021 The success of many clinical, association, or population genetics studies critically relies on properly performed variant calling step. The variety of modern genomics protocols, techniques, and platforms makes our choices of methods and algorithms difficult and there is no "one size fits all" solution for study design and data analysis. In this review,
Stepanka Zverinova, Victor Guryev
openaire +3 more sources
Canine reference genome accuracy impacts variant calling: Lessons learned from investigating embryonic lethal variants [PDF]
, 2022 Deficient homozygosity of a variant maintained in a population suggests that the variant may be embryonic lethal. We examined whole genome sequence data from 675 canids to investigate for variants with missing homozygosity and high predicted impact ...
Dog Biomedical Variant Database, Consortium +3 more
core +2 more sources
PipeIT2: Somatic Variant Calling Workflow for Ion Torrent Sequencing Data. [PDF]
, 2022 The detection of somatic genetic variants forms the cornerstone of precision oncology. Molecular diagnostics laboratories require economical and rapid protocols to generate accurate variant calls for clinical purposes. The Ion Torrent sequencing platform
Schnidrig, Désirée +2 more
core +1 more source