/INVAR2

restructures version of invar

Primary LanguageR

INVAR2

A Nextflow based software tool to run the INVAR (Integration of VAriant Reads) analysis pipeline. Previously available here.

The pipeline seeks to detect minimal residual disease signal in patient liquid biopsy data, and outputs a classifcation based on a threshold score established on a cohort of healthy samples. A general cohort size should range from around 20+ individual patients.

More details are available in the links below. Test data is available at the EGA accession numbers EGAS00001004447 and EGAS00001005246 with results available in the following publications:

[1] Wan J, Heider K, Gale D et al. ctDNA monitoring using patient-specific sequencing and integration of variant reads. Sci Transl Med. 2020;12(548). doi:10.1126/scitranslmed.aaz8084

[2] Heider K, Wan J, Gale D. ctDNA detection by personalised assays in early-stage NSCLC. MedRxiv. doi:https://doi.org/10.1101/2021.06.01.21258171

Contact: Hui.zhao@cruk.cam.ac.uk, emma-jane.ditter@cruk.cam.ac.uk

Documentation

  1. Setting up the INVAR2 pipeline.
  2. INVAR2 parameters.
  3. Running INVAR2.
  4. Results and Analysis.
  5. Indepth Technical Details.
  6. Running Instructions for Rosenfeld Lab members.
  7. FAQ's