tests/reproducible_testing/Comparison_other_methods/README.md

In DeveauP/QuantumClone: Clustering Mutations using High Throughput Sequencing (HTS) Data

Pipeline to compare sciClone, pyClone, QuantumClone and fpc's k-medoid

WARNING This pipeline is extremely long (weeks worth of computation), it is recommended to dispatch each argument of main.sh to a different node. (As it is done in the rerun for Torque infrastructures)

Editing config

All relevant paths must be set in the config file. Make sure that PyClone, sciClone, fpc, and QuantumClone are installed and available.

Results

The outputs are: - A result file for sciClone, QuantumClone and fpc giving the NMI and computation time - The output of pyClone (theoretical clones are encoded inside the chromosome number).

Plots can be found in the Plots.zip file

DeveauP/QuantumClone documentation built on Oct. 29, 2021, 8:56 a.m.