I'm on version v6.3.2 and I was reviewing the work done by the script get_rg_cns.R.
I realized that the vector cn_estimates, which is the main output, contained always onlyNA values, indicating that the estimation for small copy number segments was not working.
After further investigation, I realized that bedtools was not returning headers expected by get_rg_cns.R, specifically seg_coords were not included in the output of the bedtools coverage system call--resulting in coverages being a vector of NA values:
Best regards,
I'm on version
v6.3.2and I was reviewing the work done by the script get_rg_cns.R.I realized that the vector
cn_estimates, which is the main output, contained always onlyNAvalues, indicating that the estimation for small copy number segments was not working.https://github.com/cancerit/BRASS/blob/dd0e1c1324459c4090c598dc6a12b7b71ef34586/perl/share/Rscripts/get_rg_cns.R#L426
After further investigation, I realized that bedtools was not returning headers expected by
get_rg_cns.R, specificallyseg_coordswere not included in the output of the bedtools coverage system call--resulting incoveragesbeing a vector ofNAvalues:https://github.com/cancerit/BRASS/blob/dd0e1c1324459c4090c598dc6a12b7b71ef34586/perl/share/Rscripts/get_rg_cns.R#L401-L402
I noticed that on release
v6.3.4you make a reference tostack collisionerrors, and I wonder if that means this same bug I'm encountering.Thank you so much in advance.