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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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Any configuration preset for paftools caller? #270

Open elcortegano opened 2 years ago

elcortegano commented 2 years ago

I would like to merge VCFs generated with paftools.js from minimap. Is there any recommended preset for this among the currently available?

I am using now --config DeepVariant on the basis that to my understanding the VCFs generated are whole genome sequencing VCFs, but not 100% confident about the differences of that with the preset for other callers (e.g. gatk), or if paftools would require its own preset.

Thanks