--common_variants parameter compatibility

[carmensandoval]

Hi,

I'm afraid I've gotten myself quite confused around the use of --common_variants.

Is this option only compatible when --known_genotypes are NOT provided, or can it also be used with --known_genotypes?

My understanding is that if --known_genotypes are provided, then
a) there's no need to call variants de novo using freebayes. Instead, it will [optionally] remap, then skip the freebayes step, and rely on the provided VCF for variant information.
b) Since it will use the variants in the provided known_genotypes VCF, this is incompatible with a common_variants file.

In this sense, --common_variants can only be used if NOT using --known_genotypes (ie a genotype reference VCF)

Are these assumptions correct?

[wheaton5]

That is all correct.