mixed-sample-graphs

The obejctive of this project is to take annotated variants from mixed tissue samples and determine if they are associated with population stratification or are tumor specific.

Inputs

• Data from expressed-variant-impact:
  • variant vcf files (fully annotated variant calls from HaplotypeCaller)
  • cancer.vcf and cancer.tab (a set of prioritized cancer-relevant variants detected in the sample)
• Data from viravate2:
  • "A large table with DE results and associated variants. This would include things like gene names, logFC values, significance values, and then the variant information."

Outputs

• Data for expressed-variant-reporting:
  • See inputs docs
• Data for viravate2:
  • VCF file containig variants associated with population stratification or tumors

Flowchart

Methods

• MuTect
• somalier