WGS-Variant-Calling

This repotary is about WGS variant calling and annotation using GATK.

1. Download pre-packaged data source from Funcotator

   cd tools/

   gatk FuncotatorDataSourceDownloader --germline --validate-integrity --extract-after-download --hg38

2. Run scripts

   cd scripts/

   chmod +x variant_calling.sh ./variant_calling.sh

   chmod +x variant_filtering_annotation.sh ./variant_filtering_annotation.sh

3. Useful variant Data Sources:

   GNOMAD

   dbSNP

   ClinVar

   COSMIC