Variant Calling

This workflow calls variants in a sequence sample by aligning it to a reference genome, identifying variants and annotating them. It reimplements a publication by Koboldt et al. 2013.

A detailed description can be found on the Cuneiform website. This cookbook installs all necessary tools, downloads all necessary data, sets up Cuneiform, and places the workflow in a predetermined location. The cookbook can be run on any system in a virtual machine.

Requirements

Platforms

• Ubuntu

Chef

• Chef 12.14+

Cookbooks

• chef-cuneiform
  • chef-rebar3 -erlang
    • build-essential
    • mingw
    • seven_zip
    • windows
    • yum-epel
    • yum-erlang_solutions

Recipes

• variant-call::default updates the apt package index and runs variant-call::tools, variant-call::data, and variant-call::workflow
• variant-call::tools installs FastQC, Bowtie 2, SAMtools, VarScan, and includes the recipe variant-call::annovar.
• variant-call::annovar installs ANNOVAR
• variant-call::data includes the recipes variant-call::kgenomes, variant-call::hg38, and variant-call::annovar-db
• variant-call::kgenomes downloads two samples from the 1000 Genomes Project
• variant-call::hg38 downloads the HG38 Human reference genome from UCSC
• variant-call::annovar-db downloads the HG38 gene annotation index database for ANNOVAR
• variant-call::workflow places the Cuneiform variant calling workflow in /opt/wf

Running the Workflow

If you set up the workflow via kitchen converge, log into the machine by typing

kitchen login

Execute the workflow script by entering

cuneiform -d /opt/data /opt/wf/variant-call.cfl

Authors

• Jörgen Brandt (@joergen7) joergen.brandt@onlinehome.de

License

Apache 2.0