cccnrc / plot-vcf Goto Github PK

Originally posted by @mkyriak:

I run the command to create the plot as follows:

> createVCFplot(chr1, FASTA_FILE = assembly, CHR_NAMES = "1")
However, I am getting the following error and I don't understand which field is the "VAR_COL":

---------------------------------------------------------------------------
------------------------>   plotVCF v0.0.0.9000   <------------------------
---------------------------------------------------------------------------
    -> input VCF file: 	 ./merged-TP-samples-chr1.vcf.gz 
    -> input assembly: 	 hg38 
    -> input chromos: 	 1 
    -> input VAR_FLAG: 	 POS 
    -> input SAMPLE: 	 ALL 
    -> input FASTA: 	 ~/Documents/Analysis/ref/b37/renamed_human_g1k_v37.fasta 
    -> COLOR_SAMPLE: 	 1 groups specified
---------------------------------------------------------------------------

 -> loading FASTA file ...

 -> loading VCF file ...
  -> passed VCF file extension: gz 
  -> indexing VCF file ...
  -> reading VCF file ...
    -> VCF samples: 63 
Error in cbind(POS_COL, rownames(GENO_COL), VAR_COL, GENO_COL) : 
  object 'VAR_COL' not found

I appreciate your help.

Originally posted by @mkyriak in #1 (comment)

Hi,
After a successful plotVCF installation under R-4.2.0, the createVCFplot() function with the example shows next error message:

-> loading VCF file ...
-> passed VCF file extension: gz
-> indexing VCF file ...
Error in value[3L] : file does not appear to be bgzip'd
file: ./inst/extdata/exampleVCF.vcf.gz

I've tryed with some others bgzip'd .vcf files of my own but the same error is showed up. Any help to fix it will be welcome.
Thank you in advance for your reply.

Hi there cccnrc!

Very excited to use this package. I have successfully donwloaded it and pointed it to my .vcf file and tried to use the createVCFplot() function. However, I am getting the following error:

Error in stop_if_wrong_length("'seqnames'", ans_len) :
'seqnames' must have the length of the object to construct (1) or length 1
In addition: Warning message:
In max(VAR_Y) : no non-missing arguments to max; returning -Inf

I'm not entirely sure what this means but I'm hoping that you might! For context, I have a large .vcf file that I merged together (comprising a full plate of different samples). I am not looking at human samples, so everything is on a single chromosome but I'd like to separate the plot out by genomes instead. Is this something that you can help me with, using your package?

Thank you!

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.

Hello!

First, thanks for the wonderful and user-friendly program. I just have one question about modifying the y-axis: is there a way to manually adjust (e.g., ylim = c(0,100)) the y-axis in createVCFplot()? Any help here would be great.

Thanks!
Matthew

Hi

Will there be support for CSI indexing? Currently I'm getting errors when I run createVCFplot. It tries to index with TBI and recommends I use CSI indexing.

I'm working with a large plant genome.

Thanks.

IS it possible to plot multiple samples either all in one vcf file or load multiple vcf files at once?

Hello, I am wondering if I can change the version of the genome, so instead of hg38, can I use b37 or hg19?

Thank you!