Genome Analysis Toolkit
-
Updated
Dec 13, 2018 - R
Genome Analysis Toolkit
WDL-based pipelines
msgen: R functions for interfacing with the Microsoft Genomics service on Azure.
The repository contain directories of projects done during the bioinformatics degree program
GATK WGS workflow
Variant calling + processing pipline using GATK based in Snakemake
VariantCaller is a wrapper for the 2022 gatk & bcftools best practices + phasing with WhatsHap.
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.
Confirmation of which GATK4 versions go against VCF specifications and call missing GT as 0/0 instead of ./.
A pipeline for variant calling of Exome using GATK best practice workflow
Implementation of WGS genotyping pipeline for EFIGA FBS FAMILY dataset
A pipeline to call variants for RNASeq implemented with python.
Add a description, image, and links to the gatk topic page so that developers can more easily learn about it.
To associate your repository with the gatk topic, visit your repo's landing page and select "manage topics."