variant-calling-and-annotation

Here are 3 public repositories matching this topic...

Frederick-abichahine / Oncogenomic-Somatic-Mutation-Analysis

Comprehensive somatic mutation analysis of paired tumor-control samples using high-throughput sequencing data. This project integrates variant calling, functional annotation, and structural alteration analysis to uncover clinically relevant genomic changes, estimate tumor purity and ploidy, and explore potential therapeutic targets in oncogenomics.

shell bioinformatics r cancer somatic-variants gatk cancer-genomics igv copy-number-variation hg19 tumor-segmentation tumor-purity-estimation tpes variant-calling-and-annotation tumor-ploidy-estimation clonetv2 computational-human-genomics

Updated Jul 24, 2025
Shell

gmboowa / Bunya-ONT-Gen

Star

Bunya-ONT-Gen is a modular pipeline for analyzing Bunyavirus genomes from Nanopore metagenomic data. It supports quality control, taxonomic classification, genome assembly, variant detection & phylogenetic analysis, enabling rapid, end-to-end viral genomics

phylogenetics genome-assembly nanopore-sequencing bunyavirus variant-calling-and-annotation

Updated Sep 28, 2025
Python

MAGRabbani / wgs-variant-calling-pipeline

Star

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

bioinformatics annotation genomics variant-calling chicken wgs vep genome-assembly whole-genome-sequencing qc variant-filtration snp-analysis gatk4 gatk-bestpractices short-read-mapping gatk4-haplotypecaller short-read-sequencing variant-calling-and-annotation gatk-based-variant-calling

Updated Aug 21, 2026
Shell

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