Germline analysis pipeline

Workflows used for germline short variant discovery on WGS data following GATK best practices.

Requirements/expectations

• 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")

Outputs

• uBam
• GVCF(in progress)
• VCF?(in progress)

ToDo

• Hail tertiary analysis