gatk4-haplotypecaller

Here we are going to discuss variant calling on human datasets using GATK Best practices pipeline

Joint variant calling with GATK4 HaplotypeCaller, Google DeepVariant 1.0.0 and Strelka2, coordinated via Snakemake.

End-to-end NGS variant calling and functional annotation pipeline for Limulus polyphemus using GATK and SnpEff, with biological interpretation of high-impact immune and metabolic variants.

Optimized Python and C++ implementations of INDELseek, a Perl tool for detecting complex genetic indels in NGS data, with performance improvements, validation, and benchmarking against other variant callers.

A streamlined pipeline for germline variant calling on chromosome 11 using GATK. This repository includes workflows for data preprocessing, variant discovery, and annotation, with a focus on understanding genetic variations linked to disease-associated genes.

A reproducible, HPC-based whole genome sequencing pipeline for germline variant calling and filtering variants from raw seq reads, alignment, quality filtering, and annotation