This Snakemake pipeline implements the GATK best-practices workflow

Exome/Capture/RNASeq Pipeline Implementation using snakemake

Reusable and maintained Luigi tasks to incorporate in bioinformatics pipelines

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

Generates CWL files from the GATK documentation

Collecting Genotypes from ENA and make their SNPs

Diablo G25 - is a tool for conversion of VCF file to 23AndMe format and calculation of admixture scores from it.

VariantCaller is a wrapper for the 2022 gatk & bcftools best practices + phasing with WhatsHap.

🐍🔧 Snakemake wrappers for GATK.

Variant calling + processing pipline using GATK based in Snakemake

GATK and VARSCAN analysis pipeline

An automated tool for processing whole-exome sequencing data

Python package to parse GATK Output and extract summary statistics at mbq 0,10,20,30 and variant evaluation metrics

A public, web-based homozygosity mapping tool

This repository contains data and code for our analysis of the genome of a Plasmodium falciparum strain with reduced susceptibility to Artemisinin-Based Combination Therapy (ACT) drugs. We performed whole-genome sequencing of the HSOG3 clinical isolate and compared it with a large dataset of global P. falciparum samples.

Python utility functions for reading GATK Report files into pandas DataFrames

Convert NGS reads to analysis ready variants with GATK's ReadsPipelineSpark

Snakemake Pipeline for the Analyses of ChIP-seq data in Cancer samples

GATK variant calling for RNASeq