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7 hours ago
bdolin
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Does anyone have a sense of the prevalence of use of gVCF vs. VCF by clinical sequencing labs? (My understanding is that the use of gVCF is growing). Also, does anyone know if labs are producing gVCFs using block format vs base pair resolution format? Thanks!
AFAIK clinical labs don't even use VCF files. It's too technical for them. They'd probably have someone extract a tabular file that they can display/process.
If you're referring to research labs connected to genetic counseling services, the use of VCF vs gVCF doesn't matter at all. They're interested in (mostly rare) variants, they don't care what is used internally. And as far as I know, gVCF is still an intermediate format as far as deliverable data goes.
gVCF allows you to distinguish no-calls from reference in single samples. as a terminal format it's useful but maybe not essential.
I think the bigger trend is the slow death of joint variant calling favor of single-sample variant calling. When I see bp_resolution used it's because the developer is trying to use home-grown or non-standard tools and doesn't want to go down the rabbit hole of parsing a gVCF with reference blocks.