cccnrc
different assembler/fasta not working
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.
UPDATE:
When I take out the ASSEMBLY variable and leave it blank I get this output:
---------------------------------------------------------------------------
------------------------> plotVCF v0.0.0.9001 <------------------------
---------------------------------------------------------------------------
-> input VCF file: myFILE.vcf
-> input assembly: hg38
-> input chromos: chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX
-> input VAR_FLAG: POS
-> input SAMPLE: ALL
-> input FASTA: reference/Saccharomyces_cerevisiae.fa
-> COLOR_SAMPLE: 1 groups specified
---------------------------------------------------------------------------
-> loading FASTA file ...
Error: subscript contains invalid names
Again, still not sure what this means or what to do...I should only have 16 chromosomes and one chmrt and it's giving me 22?
If anyone could help me understand this that would be great!
I fixed that issue by inputting in my CHR_NAMES corresponding to my reference because its defaulting to human chromosome names. so something like this:
CHRS <-c("chr1","chr2","chr3","chr4","chr5","chr6","chr7","chr8","chr9","chr10","chr11","chr12","chr13","chr14","chr15","chr16")
createVCFplot( VCF, FASTA_FILE=FASTA, CHR_NAMES=CHRS)
