From what I have read, in case of trios, it would be best to perform joint genotyping across all the samples. Does varscan2 trio mode offer this functionality ?
I was cheking the varscan webpage, and saw that the trio pipeline for germline mutations would first call samtools to produce the trio mpileup file, where this is input to varscan afterwards for variant calling.
As far as I have understood, each trio is processed separately and joint genotyping across all samples is not done. Is my understanding correct?