Goal: I would like to use the program ShalloHRD (https://github.com/aeeckhou/shallowHRD) to determine the HRD status of certain samples from an Illumina cytoSNP-6850 array run.
Motivation: While I have been able to run ASCAT on the output of GenomeStudio (FullDataTable) and run scarHRD using the output of ASCAT to determine the LOH,TAI and LST scores, I would like to use ShallowHRD (instead of scarHRD) to determine the LGA score (details about the LGA score in the ShallowHRD paper).
Problems / Issues: ShallowHRD is designed to run with the output of ControlFreec (https://academic.oup.com/bioinformatics/article/28/3/423/189142?login=true#83403168) and as far as I have seen , ControlFreec cannot be run on array data and as a result I am not being able to run ShallowHRD. I am finding it difficult to modify the output of ASCAT or GenomeStudio and run ShallowHRD with it.
More precisely, I am not sure of how to interpret the "ratio" and "median ratio" values from the output of ControlFreec which is used as an input to ShallowHRD. Any help regarding this would be greatly appreciated. It would also be great to know if someone else is using CytoSNP data to infer HRD scores and if so the tools that that are using for it.