Hi Guys,

I'm performing a gender consistency check by comparing inferred gender and reported gender. My sample size is around 2700 but there are over 1000 samples with gender inconsistency. This is not a problem due to data entry error I think.
I'm using SVS golden helix to carry out the heterozygosity rate statistic and compare this with the reported gender.
The exome data were originated from affymetrix axiom 2.0 system.

Has anyone ever met this issue when using the SVS software before? Any experience or opinion that you can share please?

Thanks a lot.

Marco