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different assembler/fasta not working

Open rmormando opened this issue 1 year ago • 2 comments

Hello, I'm trying to use this tool to visualize differences in variants in yeast strains - specifically Saccharomyces cerevisiae S288C.

I tried this code:

library(plotVCF)
VCF <- "myFILE.vcf"
createVCFplot(VCF, FASTA_FILE ="reference/Saccharomyces_cerevisiae.fa", ASSEMBLY = "R64")

But I keep getting this error:

 -> please specify either default assembly (hg38/GRCh37) or CHR_NAMES to plot! (see documentation)...
Error in createVCFplot(VCF, FASTA_FILE = "reference/Saccharomyces_cerevisiae.fa",  : 

Is there something else I need to put instead of this? I'm not sure what to put for the ASSEMBLY variable - I tried "S288C" as well and still the same error.

rmormando avatar May 08 '23 20:05 rmormando