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snakemake-workflows / dna-seq-gatk-variant-calling

This Snakemake pipeline implements the GATK best-practices workflow

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Running without known-variants

silastittes opened this issue · comments

commented

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.

commented

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

commented

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

commented

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 ;-)