Karyotyping

This is the updated karyotyping pipeline for Sheltzer Lab's publications. It uses CNVKit for inferring copy numbers and a modified plotting function from the same tool.

Data files

Running the script

To run the script, you can directly run the following command once you have downloaded the data files.

    nextflow run https://github.com/sheltzer-lab/Karyotyping.git

Citations

1. Talevich, E., Shain, A.H., Botton, T., & Bastian, B.C. (2014). CNVkit: Genome-wide copy number detection and visualization from targeted sequencing. PLOS Computational Biology 12(4):e1004873
2. i) Olshen, A.B., Bengtsson, H., Neuvial, P., Spellman, P.T., Olshen, R.A., & Seshan, V.E. (2011). Parent-specific copy number in paired tumor-normal studies using circular binary segmentation. Bioinformatics 27(15):2038–46. ii) Venkatraman, E.S., & Olshen, A.B. (2007). A faster circular binary segmentation algorithm for the analysis of array CGH data. Bioinformatics 23(6):657–63

License and Attribution

This project is primarily licensed under the MIT License. However, it includes code originally developed by Eric Talevich, University of California under the Apache License, Version 2.0. See the LICENSE file for the MIT License and the NOTICE file for Apache License details.

See the NOTICE file for further attribution requirements.