Exome/Capture/RNASeq Pipeline Implementation using snakemake

HgvsGo is a program designed for analyzing "c." and "p." HGVS (Human Genome Variation Society) notations for single nucleotide variations (SNVs) and small insertions/deletions (indels) after variant calling. It serves as an alternative to tools like snpEff and VEP.

Converts snpeff annotations into MAF

Highly Open Workflow for Annotation & Ranking toward genomic variant Discovery

Multi-bAse Codon-Associated variant Re-annotatiON (MACARON)

A collection of scripts for filtering annotated variant call format files

A tool to import SnpEff annotated files to a Neo4j Graph database

Generate an interactive HTML-based report from M.tb SnpEff annotated VCF(s)

Snakemake workflow designed to annotate VCF files withe SnpEff / SniSift

The AlleleCatalog pipeline is built for generating Allele Catalog datasets using next-generation sequencing (NGS) based genetic data and metadata.

Genomic Analysis Pipeline: Automate data preprocessing, variant calling, and annotation with Snakemake. Ensure reproducibility and reliability in genomic studies.

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.

R package for mycosnp-nf to parse outputs from snpeffr to desired formats for MDB/Fungi Net

R code to parse Manta SV data annotated using SnpEff

Bioinformatics pipeline for Illumina human exome variant calling using FastQC, Trimmomatic, BWA, Samtools, Bcftools, and SnpEff. Demonstrates a reproducible workflow for NGS data analysis. #bioinformatics #genomics #variant-calling #ngs #pipeline

The PhenoDist pipeline is built for generating phenotype distributions for alleles in variant positions and utilizing statistical methods to test for variant position significance.

A pipeline for filtering annotated variant call format files