This repo is for implementing a practical workflow for variant discovery based on GATK best practices.

1. First please follow this prerequisites preparation to setup necessary tools and databases for this practice.

2. Variant calling and filtering workflow can be found here.

3. Variant annotation workflow can be found here.

1. GATK Germline short variant discovey: https://gatk.broadinstitute.org/hc/en-us/articles/360035535932-Germline-short-variant-discovery-SNPs-Indels-

2. GATK Github: https://github.com/broadinstitute/gatk