Viral genomics analysis pipelines

MyVariant.info: A BioThings API for human variant annotations

Generic human DNA variant annotation pipeline

Genomic VCF to tab-separated values

CADD-SV – a framework to score the effect of structural variants

Clinical machine-learning based interpreter of germline mutations.

A Python GUI VCF viewer for SNP, indels, and TE.

MetaDome is aimed at professionals in the (bio-)medical field of human genetics who wish to visualize the position of their mutation of interest in the context of general population-based genetic variation and provide detailed information of pathogenic variants found across homologous domain positions.

PyGeneBe: A Python client seamlessly integrating with the GeneBe platform, offering efficient annotation of genetic variants through its API, while supporting pandas, VCF file formats, and HGVS parsing

A Snakemake workflow for variant calling using GATK4 best practices

A relational database stores per sample based sequencing data.

An empirical variant annotation and data evaluation pipeline.

Repository for miscellaneous bioinformatics scripts that may be useful to others.

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

DiVA (DNA Variant Analysis) is a pipeline for Next-Generation Sequencing Exome data anlysis

Python wrapper and web-server for Ensembl VEP

WES Analysis scripts for "Immune determinants of response to neoadjuvant chemo-radiation in esophageal adenocarcinoma" publication

neural networks to score PubMed search results for similarity to evidence abstracts from ClinVar or CIViC

Customized vcf_melt script from pyvcf. Handles snpEff-annotated vcf files