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cgab-ncc / FIREVAT

FInding REliable Variants without ArTifacts
MIT License
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Error: the parameter 'vcf.file.genome' should be supported by BSgenome. #10

Closed V-Catherine closed 3 years ago

V-Catherine commented 3 years ago

Hello, I'm trying to run Firevat on a vcf from Mutect2 with genome="hg38" but I get the following error:

Error in RunFIREVAT(vcf.file = sample.vcf.file, vcf.file.genome = "hg38",  : 
  The parameter 'vcf.file.genome' should be supported by BSgenome.

I've downloaded with success hg38 using the following command: BiocManager::install("BSgenome.Hsapiens.UCSC.hg38") Do you have any idea what the problem is ? Thanks for your help Catherine

SilenWang commented 3 years ago

I ran into the same issue. Use ''BSgenome.Hsapiens.UCSC.hg38'' instead of "hg38" solve the problem.

SilenWang commented 3 years ago

I ran into the same issue. Use ''BSgenome.Hsapiens.UCSC.hg38'' instead of "hg38" solve the problem.

Well, doing so will cauese downstream problem. It seems that version 0.6.0 change the way to tell if the input genome is wrong, and this cause the problem.

I think you can either edit the downloaded source code to repair this or reinstall an older version.

V-Catherine commented 3 years ago

Thanks for your input

khb7840 commented 3 years ago

Sorry for late reply because this bug was due to the updates of BSgenome. FIREVAT checks the input genome is available for BSgenome and the name of vector for available genome version has been changed from "provider_version"(2017) to "genome" (2021). I'll upload a hotfix today.

ver 1.42.0 (2017) Screen Shot 2021-03-16 at 5 15 59 PM

ver 1.58.0 (2021) Screen Shot 2021-03-16 at 5 15 40 PM

V-Catherine commented 3 years ago

Thanks! This solves the issue :-)