SummaryThe precisionFDA Truth Challenge V2 aimed to assess the state-of-the-art of variant calling in difficult-to-map regions and the Major Histocompatibility Complex (MHC). Starting with FASTQ files, 20 challenge participants applied their variant calling pipelines and submitted 64 variant callsets for one or more sequencing technologies (~35X Illumina, ~35X PacBio HiFi, and ~50X Oxford Nanopore Technologies). Submissions were evaluated following best practices for benchmarking small variants with the new GIAB benchmark sets and genome stratifications. Challenge submissions included a number of innovative methods for all three technologies, with graph-based and machine-learning methods scoring best for short-read and long-read datasets, respectively. New methods out-performed the 2016 Truth Challenge winners, and new machine-learning approaches combining multiple sequencing technologies performed particularly well. Recent developments in sequencing and variant calling have enabled benchmarking variants in challenging genomic regions, paving the way for the identification of previously unknown clinically relevant variants.
Abstract-We examine the performance of the Karhunen-Loève transform (KLT) for transform coding applications. The KLT has long been viewed as the best available block transform for a system that orthogonally transforms a vector source, scalar quantizes the components of the transformed vector using optimal bit allocation, and then inverse transforms the vector. This paper treats fixed-rate and variable-rate transform codes of non-Gaussian sources. The fixed-rate approach uses an optimal fixed-rate scalar quantizer to describe the transform coefficients; the variable-rate approach uses a uniform scalar quantizer followed by an optimal entropy code, and each quantized component is encoded separately. Earlier work shows that for the variable-rate case there exist sources on which the KLT is not unique and the optimal quantization and coding stage matched to a "worst" KLT yields performance as much as 1.5 dB worse than the optimal quantization and coding stage matched to a "best" KLT. In this paper, we strengthen that result to show that in both the fixed-rate and the variable-rate coding frameworks there exist sources for which the performance penalty for using a "worst" KLT can be made arbitrarily large. Further, we demonstrate in both frameworks that there exist sources for which even a best KLT gives suboptimal performance. Finally, we show that even for vector sources where the KLT yields independent coefficients, the KLT can be suboptimal for fixed-rate coding.
Abstract-We examine the performance of the Karhunen-Loève transform (KLT) for transform coding applications. The KLT has long been viewed as the best available block transform for a system that orthogonally transforms a vector source, scalar quantizes the components of the transformed vector using optimal bit allocation, and then inverse transforms the vector. This paper treats fixed-rate and variable-rate transform codes of non-Gaussian sources. The fixed-rate approach uses an optimal fixed-rate scalar quantizer to describe the transform coefficients; the variable-rate approach uses a uniform scalar quantizer followed by an optimal entropy code, and each quantized component is encoded separately. Earlier work shows that for the variable-rate case there exist sources on which the KLT is not unique and the optimal quantization and coding stage matched to a "worst" KLT yields performance as much as 1.5 dB worse than the optimal quantization and coding stage matched to a "best" KLT. In this paper, we strengthen that result to show that in both the fixed-rate and the variable-rate coding frameworks there exist sources for which the performance penalty for using a "worst" KLT can be made arbitrarily large. Further, we demonstrate in both frameworks that there exist sources for which even a best KLT gives suboptimal performance. Finally, we show that even for vector sources where the KLT yields independent coefficients, the KLT can be suboptimal for fixed-rate coding.
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