Workflows used for germline short variant discovery on WGS data following GATK best practices.
- Directory of Human whole-genome paired-end sequencing data in Fastq format
- Metadata in xml format in parent directory
- Input Fastqs are expected to share the same prefix pattern ex. ("123_1", "123_2")
- uBam
- GVCF(in progress)
- VCF?(in progress)
- Hail tertiary analysis