Short|read aligner performance in germline variant identification

Short-read aligner performance in germline variant identification

Abstract. Motivation: Read alignment is an essential first step in the characterization of DNA sequence variation. The accuracy of variant- ...

Short-read aligner performance in germline variant identification

In this review, we evaluate short-read aligner performance with the goal of optimizing germline variant-calling accuracy.

Short-read aligner performance in germline variant identification

Variant calling with GATK HaplotypeCaller. (Placeholders replace actual file paths.) Page 7. Wilton and Szalay. Short-read aligner ...

Short-read aligner performance in germline variant identification

Abstract Motivation Read alignment is an essential first step in the characterization of DNA sequence variation. The accuracy of variant-calling results ...

Systematic benchmark of state-of-the-art variant calling pipelines ...

While BWA is considered a gold standard solution for short read alignment in medical genetics [5], several other aligners have been developed ...

Best Practices for Benchmarking Germline Small Variant Calls in ...

The shift from focused genotyping tests to genome sequencing enables the detection of novel sequence variants, which has fundamental implications on how these ...

GASOLINE: detecting germline and somatic structural variants from ...

showed that only a limited subset of SVs overlapped between short-read and long-read technologies (66.8% of short- and 33.5% of long-reads ...

(PDF) Benchmarking germline variant calling performance of a GPU ...

The variant calling outputs were compared to the reference and the results generated by the Burrows-Wheeler Aligner (BWA) and Genome Analysis ...

Comparative evaluation of SNVs, indels, and structural variations ...

In this study, we comprehensively evaluated the variant calling performance of short- and long-read-based SNV, indel, and SV detection algorithms.

Best practices for germline variant and DNA methylation analysis of ...

Proper alignment and preprocessing, including quality control and the use of reference genomes, are essential for reliable analysis. Tools like ...

Evaluation of Germline Structural Variant Calling Methods ... - Frontiers

In particular, we focus on the effects of read alignment, sequencing coverage, and variant allele depth on the detection and genotyping of SVs ...

Challenges in identifying large germline structural variants for ...

Additionally, Sniffles can reconstruct the haplotype structure of a sample by read-based phasing of SVs and thus determines adjacent or nested events [21].

Negligible effects of read trimming on the accuracy... | F1000Research

We show that adapter trimming has no effect on the accuracy of the best-performing variant callers (eg, DeepVariant) on whole-genome sequencing (WGS) data.

[PDF] Systematic comparison of germline variant calling pipelines ...

This study compared the performance, concordance and operating efficiency of 27 combinations of sequencing platforms and variant calling ...

Negligible effects of read trimming on the accuracy of germline short ...

We show that adapter trimming has no effect on the accuracy of the best-performing variant callers (e.g., DeepVariant) on whole-genome sequencing (WGS) data.

Systematic comparison of germline variant calling pipelines cross ...

For the variants calling performance of 12 combinations in WES datasets, all combinations displayed good performance in calling SNPs, with their ...

Performance evaluation of pipelines for mapping, variant calling and ...

4 Citations · Short-read aligner performance in germline variant identification · Identification of novel SNP markers for kinship analysis in the ...

Bioinformatics of germline variant discovery for rare disease ... - OUCI

Wilton, Short-read aligner performance in germline variant identification, Bioinformatics, № 39, с. ... Garrison, Haplotype-based variant detection from short- ...

Short Read Aligners and Variant Detection - MassGenomics

However, these assessments bring into focus the key issue surrounding short read alignment for variant detection – finding the balance between ...

RNAseq short variant discovery (SNPs + Indels) - GATK

Because RNA aligners have different conventions than DNA aligners, we need to reformat some of the alignments that span introns for HaplotypeCaller. This step ...