Contents

Welcome to the PsychCore NGS Variant-Calling Pipeline documentation!

About

The following NGS pipeline was developed by the UCSF Psychiatry Bioinformatics Core (PsychCore) team to call variants on large cohorts of human sequencing data. The current build is can run on either whole genome or whole exome/targeted sequencing data. This build can also call variants based on either reference genome GRCh37 (hg19) or GRCh38 (hg38). Please note that this pipeline is still being developed.

• Pipeline Overview
  • Genomics Workflow
  • Pipeline Infrastructure
  • A Note about Sentieon
• Getting Started
  • Creating and Setting up your Amazon Web Services (AWS) Account
  • Download and Upload Reference Files to S3
  • Obtain a Sentieon License File
  • Install Conda and your Dev Environment
  • Next Steps
• Configuration
  • Your Pipeline Run
• Running the Pipeline and its Output
  • Starting a Run
  • Pipeline Output
• Contact Us
  • Our Team