Homologous Recombination Deficiency score

[ericblanc20]

The cancer exome ring trial requires the pipeline to compute a score for homologous recombination deficiency.

The R package scarHRD provides such a score, and it is the software recommended for that purpose by the ring trial organisers.

We are not aware of alternatives to scarHRD, certainly not computing the individual scores (loss of heterozygosity, telomeric allelic imbalances and large scale transitions) together.

However, there are significant drawbacks to scarHRD:

• The software is only available through github, it is neither in CRAN nor in Bioconductor nor in Bioconda.
• The software relies on obsolete packages (sequenza and a modified version of the deprecated copynumber Bioconductor package).
• Documentation and benchmarks are very limited