How do I run deTiN?

DeTiN runs as a standalone python program. The Github includes example data for running deTiN.

example command line using this data:

python --mutation_data_path example_data/HCC_10_90.call_stats.pon_annotated.txt --cn_data_path example_data/HCC-1143_100_T-sim-final.acs.seg --tumor_het_data example_data/HCC_10_90.tumor.hets.tsv --normal_het_data example_data/HCC_10_90.normal.hets.tsv --exac_data_path example_data/ExAC.vcf --output_name 10_percent_TiN_simulation
The mutation input was generated using MuTect:

and the copy number data was generated using GATK4CNV:

Cell line simulation data:

Bams used in the publication for the in-vitro simulation can be downloaded from the FireCloud library:

For guidance on downloading data see: