PacificBiosciences/paraphase

Joint structural variant and copy number variant caller for HiFi sequencing data

Bayesian haplotype-based genetic polymorphism discovery and genotyping.

T1K is a versatile methods to genotype highly polymorphic genes (e.g. KIR, HLA) with bulk or single-cell RNA-seq, WGS or WES data.

Inference of ploidy and heterozygosity structure using whole genome sequencing data

DELLY2: Structural variant discovery by integrated paired-end and split-read analysis

Reusable genomic evidence for research and analysis tools: exact read evidence, portable datasets, and managed analyzers.

DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data.

Copy number variant detection from targeted DNA sequencing

fast sample-swap and relatedness checks on BAMs/CRAMs/VCFs/GVCFs... "like damn that is one smart wine guy"