Best practices for benchmarking germline small-variant calls in human genomes
Standardized benchmarking approaches are required to assess the accuracy of variants
called from sequence data. Although variant-calling tools and the metrics used to assess …
called from sequence data. Although variant-calling tools and the metrics used to assess …
NGSEP3: accurate variant calling across species and sequencing protocols
Motivation Accurate detection, genotyping and downstream analysis of genomic variants
from high-throughput sequencing data are fundamental features in modern production …
from high-throughput sequencing data are fundamental features in modern production …
Measuring, visualizing, and diagnosing reference bias with biastools
Many bioinformatics methods seek to reduce reference bias, but no methods exist to
comprehensively measure it. Biastools analyzes and categorizes instances of reference …
comprehensively measure it. Biastools analyzes and categorizes instances of reference …
Reproducible integration of multiple sequencing datasets to form high-confidence SNP, indel, and reference calls for five human genome reference materials
Benchmark small variant calls from the Genome in a Bottle Consortium (GIAB) for the
CEPH/HapMap genome NA12878 (HG001) have been used extensively for developing …
CEPH/HapMap genome NA12878 (HG001) have been used extensively for developing …
vcfdist: accurately benchmarking phased small variant calls in human genomes
T Dunn, S Narayanasamy - Nature Communications, 2023 - nature.com
Accurately benchmarking small variant calling accuracy is critical for the continued
improvement of human whole genome sequencing. In this work, we show that current …
improvement of human whole genome sequencing. In this work, we show that current …
Probably correct: rescuing repeats with short and long reads
M Cechova - Genes, 2020 - mdpi.com
Ever since the introduction of high-throughput sequencing following the human genome
project, assembling short reads into a reference of sufficient quality posed a significant …
project, assembling short reads into a reference of sufficient quality posed a significant …
Bioinformatics workflows for genomic variant discovery, interpretation and prioritization
OU Sezerman, E Ulgen, N Seymen… - Bioinformatics tools for …, 2019 - books.google.com
Next-generation sequencing (NGS) techniques allow high-throughput detection of a vast
amount of variations in a cost-efficient manner. However, there still are inconsistencies and …
amount of variations in a cost-efficient manner. However, there still are inconsistencies and …
[HTML][HTML] Principles and recommendations for standardizing the use of the next-generation sequencing variant file in clinical settings
A national workgroup convened by the Centers for Disease Control and Prevention
identified principles and made recommendations for standardizing the description of …
identified principles and made recommendations for standardizing the description of …
Alternate-locus aware variant calling in whole genome sequencing
Background The last two human genome assemblies have extended the previous linear
golden-path paradigm of the human genome to a graph-like model to better represent …
golden-path paradigm of the human genome to a graph-like model to better represent …
Improving variant calling using population data and deep learning
Large-scale population variant data is often used to filter and aid interpretation of variant
calls in a single sample. These approaches do not incorporate population information …
calls in a single sample. These approaches do not incorporate population information …