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dnanexus-rnd / GLnexus

Scalable gVCF merging and joint variant calling for population sequencing projects
Apache License 2.0
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What assumptions remain if one deactivate the specific filters #231

Open ghost opened 4 years ago

ghost commented 4 years ago

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 commented 4 years ago

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.