Rerun somatic Tumor with different min_allele_fraction Parameter

[apastore]

Hi Brad, I have a question: I have to rerun a tomor/normal paired variant calling project with a lower min_allele_fraction. I still have the work directory. Could you tell me what I should delete to rerun only the minimal possible part of the variant call pipeline?

Thanks for your help.

[chapmanb]

Thanks for the question. In general, removing the directories you want to regenerate is all you need to do. So I'd suggest removing any of the top level directories for anything listed in variantcallers. If you want to also regenerate gemini databases, remove gemini and if you need to redo a validation, remove validate. Hope this helps with the re-run.

[apastore]

Thanks ! Since is an presto large exome project, i was wondering at which level the allele fraction filter is apply and remove only those part of the variantcallers.

Thanks a lot.

Sent from my iPhone

On Jul 21, 2017, at 3:58 AM, Brad Chapman notifications@github.com wrote:

Thanks for the question. In general, removing the directories you want to regenerate is all you need to do. So I'd suggest removing any of the top level directories for anything listed in variantcallers. If you want to also regenerate gemini databases, remove gemini and if you need to redo a validation, remove validate. Hope this helps with the re-run.

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[chapmanb]

allellic fraction is a flag passed to the genotypers that support it: FreeBayes, VarDict, MuTect, VarScan. That means you need to clean the full variantcaller directories to let them recall. Hope this helps.