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Title[redir]:
An efficient and scalable analysis framework for variant extraction and refinement from population-scale DNA sequence data - PMC
Description:
The analysis of next-generation sequencing data is computationally and statistically challenging because of the massive volume of data and imperfect data quality. We present GotCloud, a pipeline for efficiently detecting and genotyping high-quality ...
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Keywords {π}
data, variant, gotcloud, sequencing, variants, filtering, samples, genotype, svm, sequence, quality, genomes, sample, tstv, gatk, pipeline, snps, pmc, refinement, lowcoverage, article, small, genome, analysis, project, calling, sensitivity, google, scholar, doi, exome, step, results, pubmed, studies, fig, files, free, features, table, supplemental, based, false, memory, exomes, target, alignment, computational, reads, number,
Topics {βοΈ}
[google scholar] cortes haplotype-aware refinement depends haplotype-aware genotype refinement pmc beta search high-throughput sequence data quantile-normalized feature space large-scale sequencing studies large-scale sequence data population-scale exome sequencing accurate genotype/haplotype inference large-scale sequencing projects large-scale sequencing data haplotype-based genotype refinement binary sequence aligned/mapped smaller-sized sequencing studies genome-wide association studies machine-learning-based filtering machine-learning-based approach sample-level quality control single-base sequencing error reduces false-positive associations high-performance computing clusters specific target ts/tv human protein-coding variants analyzing ts/tv ratios improving genotype accuracy made large-scale sequencing memory-bound computing environments alter protein sequence supplementary materials included leveraging haplotype information array-based genotype data model-transfer filtering appears haplotype-aware refinement low-coverage data increased org/cgi/doi/10 high-quality variants calls machine-learning techniques substantially improves accuracy support vector machine genotyping high-quality variants raw sequence reads unlike low-coverage genomes horizontal axis represents amazon web services genotypes high-quality snps model-transfer filtering trained time-consuming pileup step medical sequencing studies raw sequence data
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