Technology Networks

Deep Learning for Variant Calling: How DeepVariant and Neural Networks Are Improving Genomic Accuracy

Deep learning variant calling has transformed genomic accuracy. Discover how DeepVariant works, outperforms classical tools, ...
GitHub

tianshilu/QBRC-Somatic-Pipeline

The QBRC mutation calling pipeline is a flexible and comprehensive pipeline for mutation calling that has glued together a lot of commonly used software and data processing steps for mutation calling.
gut.bmj

Whole exome sequencing analyses reveal gene–microbiota interactions in the context of IBD

Objective Both the gut microbiome and host genetics are known to play significant roles in the pathogenesis of IBD. However, the interaction between these two factors and its implications in the ...
GitHub

BaitsTools: software for hybridization capture bait design

Ruby >= 2.4.1 is required as of BaitsTools version 1.7.0. BaitsTools versions <= 1.6.8.1 are compatible with Ruby >= 2.0.0. General instructions for installation ...
Frontiers

BRCA1/2 variant landscape and clinical correlates in high-risk breast cancer patients from Eastern China

Variants were called using GATK HaplotypeCaller and FreeBayes, followed by variant filtering. The thresholds were set at QD > 2.0 and FS < 200 (GATK) and QUAL > 10 (FreeBayes). The VCF files from both ...
Frontiers

A novel de novo QRICH1 variant causing Ververi–Brady syndrome with infantile epileptic spasms syndrome: clinical and genetic analysis

Data quality control and target region coverage evaluation were performed using bamdst (v1.0.9) and QualiMap (v2.2.1). Variant calling for single nucleotide variants (SNVs) and small ...