Basic workflow probabilistic inference of clonal HLA LOH.
Refer to example input files under data/.
- Tree edges: Two-column table specifying the clonal phylogeny (0 = root)
- Clonal prevalences: Table of clonal prevalences
- Ploidy and cellularity (similar input format to LOHHLA)
- Read stats: Unique read counts from flagstat
- HLA loss table: Output of LOHHLA, but tab-separated
- CPN table: Output of LOHHLA, but tab-separated
- python2.7
- numpy
- pandas
- pymc3
- theano
- matplotlib
- Add versions
- Properly document