Currently, NA12878 (a female sample) is used as an acceptor. However, chrX variants from male patients are included in the validation set. These are called as hemizygous alternate in the male donor, but will be called as homozygous alternate in the female acceptor, making overall validation performance a bit tricky due to this genotyping difference.
A proposed solution is to create an autosome-only validation set, and a sex-chromosome-only validation set, that way we do not have to remake entire validation sets due to donor/acceptor gender mismatches.
Currently, NA12878 (a female sample) is used as an acceptor. However, chrX variants from male patients are included in the validation set. These are called as hemizygous alternate in the male donor, but will be called as homozygous alternate in the female acceptor, making overall validation performance a bit tricky due to this genotyping difference.
A proposed solution is to create an autosome-only validation set, and a sex-chromosome-only validation set, that way we do not have to remake entire validation sets due to donor/acceptor gender mismatches.