Results 51 to 60 of about 709,139 (287)
Detailed comparison of two popular variant calling packages for exome and targeted exon studies [PDF]
PeerJ, 2014 The Genome Analysis Toolkit (GATK) is commonly used for variant calling of single nucleotide polymorphisms (SNPs) and small insertions and deletions (indels) from short-read sequencing data aligned against a reference genome.
Charles D. Warden +3 more
doaj +2 more sources
The impact of post-alignment processing procedures on whole-exome sequencing data [PDF]
Genetics and Molecular Biology, 2020 The use of post-alignment procedures has been suggested to prevent the identification of false-positives in massive DNA sequencing data. Insertions and deletions are most likely to be misinterpreted by variant calling algorithms.
Murilo Guimarães Borges +3 more
doaj +1 more source
, 2015 Results from variant calling in the three workflows MiSEQ Reporter 2.1.43 (GATK variant caller), CLC Genomics Workbench 5.51 (Probalistic variant caller) and the in-house custom pipeline (Freebayse variant caller).
Viktor Ljungström (778129) +5 more
core +1 more source
Scaling a Variant Calling Genomics Pipeline with FaaS
Proceedings of the 9th International Workshop on Serverless Computing, 2023 With the escalating complexity and volume of genomic data, the capacity of biology institutions' HPC faces limitations. While the Cloud presents a viable solution for short-term elasticity, its intricacies pose challenges for bioinformatics users. Alternatively, serverless computing allows for workload scalability with minimal developer burden. However,
Aitor Arjona +8 more
openaire +4 more sources
Benchmarking of single nucleotide somatic variant calling [PDF]
, 2017 Cancer, which affects hundreds of thousands of people worldwide every year and costs billions in treatment, is a disease caused by mutations that arise in somatic cell lines and contribute to abnormal and pathological behaviors and growth in cells. These
Derryberry, Dakota Zipporah
core +1 more source
, 2018 These are scripts we used for SNP variant calling. The locuslist provides a list of specific SNPs which were called for this analysis.
Forister, Matt +11 more
core +1 more source
Pediatric Blood &Cancer, EarlyView.ABSTRACT Background Children with sickle cell anemia (SCA) in low‐income settings are at risk of severe malnutrition, but optimal nutritional management has not been established. We evaluated an intensified ready‐to‐use therapeutic food (RUTF) regimen in children with persistent severe malnutrition after initial treatment and assessed whether early ...
Safiya Gambo +9 more
wiley +1 more source
Variant Calling in the Dark Genome: Benchmarking SNV Calls in the Flanks of Structural Variants
Genomics, Proteomics & BioinformaticsAbstract Single nucleotide variant calling protocols routinely discard calls in the regions immediately flanking structural variants (often 50 bp either side) because it is technically challenging to call them accurately. Although there are undoubtedly true variants of interest in these regions, many remain hidden as they are ...
Ningxin Dang +7 more
openaire +1 more source
Variant callers for next-generation sequencing data: a comparison study. [PDF]
PLoS ONE, 2013 Next generation sequencing (NGS) has been leading the genetic study of human disease into an era of unprecedented productivity. Many bioinformatics pipelines have been developed to call variants from NGS data.
Xiangtao Liu +4 more
doaj +1 more source
Pediatric Blood &Cancer, EarlyView.ABSTRACT Background Latino children are projected to make up nearly one‐third of United States (US) children by 2060, and many of their caregivers speak Spanish. Prior survey research has documented communication difficulties for Spanish‐speaking caregivers of children with cancer, but contemporary qualitative data are limited.
Jenny Ruiz +6 more
wiley +1 more source