Hello

I am running oncodrivefml for human exomes. I have specified in my config file:

[genome]
build = 'hg38'

[signature]
# Choose the method to calculate the trinuclotide singature:
method = 'complement'

# Choose the classifier (categorical value for the signature):
classifier = 'SAMPLE'

and a score file (hg38 version). I also specify a regions file on the command line.

The documentation states "Signature correction is done using precomputed counts of whole genome and whole exome of HG19 reference genome." Is this true even if I have specified hg38 in my config file? If I build my own exome signatures file using bgsignatures, which parameters do you recommend using? e.g.

bgsignature count -r regions.bed -g hg38 -s 3 -o hg38_kmer_counts.out
Do you recommend --collapse or --no-collapse?

Thanks