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 deTiN.py --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: http://archive.broadinstitute.org/cancer/cga/mutect

and the copy number data was generated using GATK4CNV:

https://gatkforums.broadinstitute.org/gatk/discussion/9143/how-to-call-somatic-copy-number-variants-using-gatk4-cnv

Cell line simulation data:

Bams used in the publication for the in-vitro simulation can be downloaded from the FireCloud library:  https://portal.firecloud.org/#workspaces/broad-firecloud-testing/deTiN_release_data

For guidance on downloading data see: https://storage.googleapis.com/detin-data-release/README_crsp_ice_somatic_validation.txt