dna-seq-gatk-variant-calling icon indicating copy to clipboard operation
dna-seq-gatk-variant-calling copied to clipboard

Published 20 hours ago • verified publisher icon snakemake-workflows

Running without known-variants

Open silastittes opened this issue 4 years ago • 3 comments

Thank you for making these workflows! In many cases I work with samples without previously known variants available. Is it possible to configure this workflow to skip steps that rely on having known-variants? I attempted this by making an empty file. Unsurprisingly, this failed.

silastittes avatar Feb 28 '20 22:02 silastittes

Hi, same use case here... Did you manage to find a workaround? Thanks!

knokknok avatar Mar 27 '21 22:03 knokknok

I did not! You might give this new pipeline a try. The recalibration step appears to be optional. https://arxiv.org/abs/2103.15167

silastittes avatar Apr 08 '21 22:04 silastittes

Thanks @silastittes for mentioning my pipeline here! Indeed, it does not require known variants, and also offers a lot of other tools and settings. Maybe it helps @knokknok as well ;-)

lczech avatar Jul 20 '22 06:07 lczech