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.

Highly Open Workflow for Annotation & Ranking toward genomic variant Discovery

Converts snpeff annotations into MAF

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

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

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

A pipeline for filtering annotated variant call format files

RNA-seq pipeline in R/Bash enables QC, alignment, read counting, and differential expression using Bioconductor; reproducible workflow on Ubuntu with Conda. 🐙

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

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.

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

A detailed bioinformatics workflow for Whole Exome (WES) and Targeted Region Sequencing (TRS) data analysis, covering quality control, alignment, variant calling, annotation, and interpretation using tools like FastQC, Trim Galore, BWA, SAMtools, GATK, and SnpEff.

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

R code to parse Manta SV data annotated using SnpEff

Automated variant annotation pipeline, and curated OMIM and ClinVar SNV datasets, developed by Martina Debnath.