BAyesian Model SElection for Inferring the subclonal history of tumor samples
usage: bamse.py [-h] [-e error] [-nc max_clusts] [-s sparsity] [-n n_trees] [-t top_trees] inputfile [inputfile ...]
inputfile: a tab delimited file including with somatic mutations as rows and columns named sample_name.ref for reference reads and sample_name.var for each sample
sequencing_error: sequencing error rate for ref -> var and vice versa
sparsity: a number between zero and one that represent the prior probability that any subclone is absent at any sample, negative values are interpreted as zero
max_clusters: maximum number of clusters to consider
num_trees: number of alternative clusterings to consider for each possible number of clusters
top_trees: number of top solutions to produce output for
dot files for visualization with graphviz
text files and pickle files to load with python, one per tree, describing the trees.