HaplotypeCaller ERC option
I am interested in knowing if there is a way to emit all sites when the input file contains multiple samples in HaplotypeCaller. I have tried the
option emitRefConfidence but got an error as this option can only be used with a single sample. It is very important for calculating general population genetic parameters to know the total number of invariant as well as variant sites. Is there a way of doing this that I am missing?
Many thanks for your time,