Dear Bob Handsaker
As you said that genotyping gains power by genotyping many samples together. However, the process of generating the summary metadata by using SVPreprocess will take a long time when I have several hundreds of samples. Thus, I wonder that when I run SVPreprocess and SVGenotyper for each sample and then using bcftools merge to merge the individual VCF file together (I have candidate variants, only genotyping not discovery), will there be much different from genotyping many samples together? Thank you.
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