Pairtree is a method for reconstructing cancer evolutionary history in individual patients, and analyzing intratumor genetic heterogeneity. Pairtree focuses on scaling to many more cancer samples and cancer cell subpopulations than other algorithms, and on producing concise and informative interactive characterizations of posterior uncertainty.
MIT License
37
stars
11
forks
source link
FloatingPointError: invalid value encountered in true_divide #14
I've been getting the following error when running Pairtree using default parameters with the attached example data.
File "/hpf/largeprojects/adam/projects/subclonal_pipeline/scripts/pairtree/bin/../lib/phi_fitter_lol.py", line 47, in _fit_etas
phi_implied = (var_reads / (ref_reads + var_reads)) / omega
FloatingPointError: invalid value encountered in true_divide
This error takes place during the sampling trees stage. I have noticed that this error usually occurs in datasets with a high proportion of mutations that have a "var_read_prob" of 0.
I wanted to confirm if a SNV mutation that exists in a segment with an estimated minor copy number of 0 and a major copy number of 2 should have a var_read_prob value of 0. If so, what is the best way to correct the above error when there are many mutations that have a var_read_prob value of 0 in the input data?
example_data.zip
I've been getting the following error when running Pairtree using default parameters with the attached example data.
This error takes place during the sampling trees stage. I have noticed that this error usually occurs in datasets with a high proportion of mutations that have a "var_read_prob" of 0.
I wanted to confirm if a SNV mutation that exists in a segment with an estimated minor copy number of 0 and a major copy number of 2 should have a var_read_prob value of 0. If so, what is the best way to correct the above error when there are many mutations that have a var_read_prob value of 0 in the input data?