Download the CBaSEv1.2.zip file using the link above or from https://weghornlab.net/software.html, unzip it and run the following command within the folder:
python CBaSE_v1.2.py INFILE VCF BUILD CMODE MODEL OUTNAME
Command line arguments:
(1) INFILE: Path to file containing somatic mutation data.
(2) VCF: 1 = input format is vcf, 0 = input format is CBaSE v1.1 input format.
(3) BUILD: One of {hg19, hg38} (not used when VCF==0).
(4) CMODE: 3 = trinucleotides, 5 = pentanucleotides, 7 = heptanucleotides.
(5) MODEL: Model choice for P(lambda): 0 = all, 1 = Gamma (G), 2 = InverseGamma (IG), 3 = Exp+G, 4 = Exp+IG, 5 = G+G, 6 = G+IG.
(6) OUTNAME: Name of data set.
Output file format:
CBaSE writes the output, including the q-values for negative and positive selection, into the file "q_values_OUTNAME.txt", located in the folder "Output".
For more details, visit https://github.com/weghornlab/CBaSE.
The CBaSE v1.1 web tool can be found here. Note that CBaSE v1.2 is only available as a standalone python script, downloadable here.
If you find our tool useful, please cite Weghorn & Sunyaev, Nature Genetics (2017).