C++ library and cmdline tools for parsing and manipulating VCF files with python and zig bindings
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Mar 20, 2026 - C++
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haplotypecaller
Here are 8 public repositories matching this topic...
The Pharmacogenomic Clinical Annotation Tool
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Sep 1, 2026 - Java
Smart and Accurate Polishing of Phased Haplotypes Integrating Read Enhancements (SAPPHIRE)
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Mar 21, 2026 - C++
Nextflow pipeline for GATK best practices (HaplotypeCaller)
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Jul 16, 2019 - Nextflow
A BioWDL workflow for generating gVCF files from BAM files.
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Apr 1, 2020 - WDL
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.
bioinformatics snps vcf gatk variant-calling bam population-genetics samtools bwa genome-analysis indels bcftools variant-annotation reference-genome exome-sequencing 1000genomes snpeff haplotypecaller human-genome gatk4-haplotypecaller
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Nov 26, 2024 - R
Germline variant calling pipeline
bioinformatics snakemake python3 variants variant-calling bwa germline clinical-research varscan pindel vardict germline-variants deepvariant vusion haplotypecaller
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Aug 27, 2025 - Python
Historical NECSTLab research prototype accelerating GATK PairHMM on NVIDIA GPUs with CUDA; IEEE EUROCON 2023 second-prize project.
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Aug 7, 2026 - Cuda
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