germline

Analysis pipeline to detect germline or somatic variants (pre-processing, variant calling and annotation) from WGS / targeted sequencing

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

Detect germline or somatic variants from normal or tumour/normal whole-genome or targeted sequencing

Generic human DNA variant annotation pipeline

Ready-to-run AWS Deadline Cloud samples for rendering (Maya, Blender, Houdini, Nuke); physical AI (robotics, autonomous driving simulation, MuJoCo, CARLA); synthetic data generation; generative AI video; and bioinformatics.

VisCap is an open flexible, software program targeted to clinical laboratories for inference and visualization of germline copy number variants (CNVs) from targeted next-generation sequencing data. For algorithmic details, see Pugh TJ et al. Genet Med. 2016 Jul;18(7):712-9.

A nextflow pipeline for calling and annotating small germline variants from short DNA reads for WES and WGS data

Nextflow bioinformatics pipeline for large-scale analysis of Multiple Myeloma genomes

nRex: Germline and somatic single-nucleotide, short indel and structural variant calling

A parser for immune receptor gene data, mainly IMGT references

Cross-reference 23andMe raw variant file with ClinVar

Workflow for biological validation of germline SNP and indel variant datasets.

pyAmpli: an amplicon-based variant filter pipeline for targeted enriched resequencing data

CAYA Analysis

A modular Nextflow DSL2 pipeline implementing the GATK Best Practices for germline variant discovery from FASTQ preprocessing to functional variant annotation using Ensembl VEP.

CAYA Analysis

This package provide rest api for azure cosmos germlin graph data base query access

Germline variant calling pipeline

Germline variant-calling pipeline (BWA/GATK/bcftools) in Nextflow, with Docker/Singularity profiles — security-reviewed

CallForge — a reproducible Nextflow pipeline for targeted-capture germline analysis: FASTQ to annotated joint callset (SNV/indel, CNV, STR, paralog-aware) with cohort QC, GIAB benchmarking, and rare-variant burden testing. Pairs with CaptureForge; runs standalone.