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by jghn 3885 days ago
You're not going to VCF on a whole genome in several hours.
2 comments

With particular hardware and software you can. Edico Dragen claims speeds for bcl -> vcf of 20 minutes [1]. With Microsoft Research's snap aligner and 450GB of memory you can get whole genome alignment in ~30 minutes and then variant calling can be done in a couple hours.

1. http://www.edicogenome.com/dragen/dragen-gp/

Could you please elaborate on this?