Marek Cmero

Each break-end pair that compose an inversion will be +/+ and -/-. Have a look at [Supplementary Figure 8](https://www.nature.com/articles/s41467-020-14351-8#Sec41) of the paper.

The vaf1/vaf2 values are the same as the adjusted_vaf1/2 found in the [filter output](https://github.com/mcmero/SVclone?tab=readme-ov-file#filter-output). These adjusted support/norm values are the ones used by ccube for clustering. The filter output also...

The `ccube_sv_input.txt` file does not contain CCFs, it is the input to the clustering algorithm that infers CCF (as well as clusters, multiplicity etc.). Please see the [cluster output documentation](https://github.com/mcmero/SVclone?tab=readme-ov-file#cluster-output).

You are right, the `subclonal_structure.txt` file only contains the proportion and not the CCF (documentation corrected in cb4659f). This file contains the cluster level information you are looking for (SVs...

Which version of bpipe are you running? I believe this was due to a change between bpipe versions in the way that parameters values are handled from text files.

Try version 0.9.12, you can constrain this like so (with minite env loaded): ``` mamba install -c conda-forge -c bioconda bpipe=0.9.12 ``` I really should pin the right version in...

I've tried testing in a fresh environment using the bpipe version that is installed by default (0.9.13) and couldn't replicate the error. Can you post the run command and output?

This should be fixed in [MINTIE v0.4.3](https://github.com/Oshlack/MINTIE/releases/tag/v0.4.3). Please reopen with an error log if you run into the problem again with this version.