processing female samples with CNVkit upstream of coral

[eesiribloom]

I am running CoRAL on female samples. I am following the script provided to generate .cns files from cnvkit using the reference provided hg38full_ref_5k.cnn

My CNVkit output states it is assuming male in some samples despite them being female.

I have also tried to remove chrY entries from hg38full_ref_5k.cnn but this does not change the result.

Will this affect how CNAs are called on chrX and therefore the downstream analysis with CoRAL or can I ignore this and proceed?

[jluebeck]

I believe the consequence is typically negligible given the amplified nature of the regions studied by CoRAL, but we can attempt to resolve this behavior in the future.

Thanks,
Jens

[eesiribloom]

Thanks for the response.
Would you be able to describe how the hg38full_ref_5k.cnn was generated?
I can't seem to generate a CNV_SEED.bed file from it unlike with my own generated flat reference produced by CNVkit.