What assumptions remain if one deactivate the specific filters

[ghost]

Hello,

let us say we are using GLNexus for joint-calling of variants. If we specify a yaml that has no criteria (so, no minimal AQ, etc ...) how does the joint-calling still differ from, for example, bcftools merge ?

thank you

[mlin]

I'd expect the representations of overlapping alleles and multi-allelic sites to differ somewhat since there isn't a unique solution to describing them. We're actually even thinking of changing how GLnexus itself does this, discussed on #210.