The variant call format and VCFtools [PDF]
Bioinformatics, 2011 Abstract Summary: The variant call format (VCF) is a generic format for storing DNA polymorphism data such as SNPs, insertions, deletions and structural variants, together with rich annotations. VCF is usually stored in a compressed manner and can be indexed for fast data retrieval of variants from a range of positions on the ...
Petr Danecek +11 more
openaire +4 more sources
Structural variant calling: the long and the short of it [PDF]
Genome Biology, 2019 AbstractRecent research into structural variants (SVs) has established their importance to medicine and molecular biology, elucidating their role in various diseases, regulation of gene expression, ethnic diversity, and large-scale chromosome evolution—giving rise to the differences within populations and among species. Nevertheless, characterizing SVs
Medhat Mahmoud +5 more
openaire +5 more sources
Evaluating the accuracy of variant calling methods using the frequency of parent-offspring genotype mismatch. [PDF]
, 2022 The use of next-generation sequencing (NGS) datasets has increased dramatically over the last decade, but there have been few systematic analyses quantifying the accuracy of the commonly used variant caller programs.
Lind, Brandon M. +15 more
core +2 more sources
IBEXCluster/Rice-Variant-Calling: HPC-GVCW
, 2023 <p><span>The objective of this proposed workflow is to </span><span>automate and accelerate the variant calling </span><span>at </span><span>high-performance computing (HPC)</span><span> ...
Rivera, Luis +6 more
core +1 more source
Variant Calling Parallelization on Processor-in-Memory Architecture [PDF]
2020 IEEE International Conference on Bioinformatics and Biomedicine (BIBM), 2020 Abstract In this paper, we introduce a new combination of software and hardware PIM (Process-in-Memory) architecture to accelerate the variant calling genomic process. PIM translates into bringing data intensive calculations directly where the data is: within the DRAM, enhanced with thousands of processing units. The energy consumption,
Lavenier, Dominique +2 more
openaire +3 more sources
Comparison of variant calling methods for whole genome sequencing data in dairy cattle [PDF]
, 2014 Accurate identification of SNPs from next-generation sequencing data is crucial for high-quality downstream analysis. Whole genome sequence data of 65 key ancestors of genotyped Swiss dairy populations were available for ...
Baes, Christine F. +12 more
core +2 more sources
GeDi: applying suffix arrays to increase the repertoire of detectable SNVs in tumour genomes
BMC Bioinformatics, 2020 Background Current popular variant calling pipelines rely on the mapping coordinates of each input read to a reference genome in order to detect variants.
Izaak Coleman +5 more
doaj +1 more source
Evaluation of variant calling for cpn60 barcode sequence-based microbiome profiling.
PLoS ONE, 2020 Amplification and sequencing of conserved genetic barcodes such as the cpn60 gene is a common approach to determining the taxonomic composition of microbiomes.
Sarah J Vancuren +3 more
doaj +1 more source
HELLO: improved neural network architectures and methodologies for small variant calling
BMC Bioinformatics, 2021 Background Modern Next Generation- and Third Generation- Sequencing methods such as Illumina and PacBio Circular Consensus Sequencing platforms provide accurate sequencing data.
Anand Ramachandran +3 more
doaj +1 more source
Boosting variant-calling performance with multi-platform sequencing data using Clair3-MP
BMC Bioinformatics, 2023 Background With the continuous advances in third-generation sequencing technology and the increasing affordability of next-generation sequencing technology, sequencing data from different sequencing technology platforms is becoming more common.
Huijing Yu +4 more
doaj +1 more source