Question: Seq Array converting VCF to GDS using seqVCF2GDS, unable to find file problems with vcf.fn
0
gravatar for cav3gh
8 months ago by
cav3gh0
cav3gh0 wrote:

So, I can read the vcf file into R using read.vcf, but I cannot seem to get seqVCF2GDS to work.  I have tried the following code:

> vcf_test1 <- read.vcf("/Users/Desktop/batch_1.vcf")
Reading 10000 / 10000 loci.
Done.

> vcf.fn <- "C:/Users/Desktop/batch_1.vcf"
> seqarray_test1 <- seqVCF2GDS(vcf.fn)
Error in stopifnot(is.character(out.fn), length(out.fn) == 1L) : 
  argument "out.fn" is missing, with no default
> vcf.fn = "C:/Users/Desktop/batch_1.vcf"
> seqarray_test1 <- seqVCF2GDS(vcf.fn, "mangrove.gds")
Error in file(vcf.fn[1L], open = "rt") : cannot open the connection
In addition: Warning message:
In file(vcf.fn[1L], open = "rt") :
  cannot open file 'C:/Users/Desktop/batch_1.vcf': No such file or directory
 

I am not sure what I am doing wrong

seqarray • 168 views
ADD COMMENTlink modified 8 months ago by Stephanie M. Gogarten600 • written 8 months ago by cav3gh0
Answer: Seq Array converting VCF to GDS using seqVCF2GDS, unable to find file problems w
0
gravatar for zhengx
8 months ago by
zhengx20
United States
zhengx20 wrote:

Please make sure your file exists.

You might try

file.size(vcf.fn)

to see whether it returns the correct size of that VCF file.

 

ADD COMMENTlink written 8 months ago by zhengx20
Answer: Seq Array converting VCF to GDS using seqVCF2GDS, unable to find file problems w
0
gravatar for Stephanie M. Gogarten
8 months ago by
University of Washington
Stephanie M. Gogarten600 wrote:

Note that you are using two different paths in the example that worked (with read.vcf) and the example that did not work, so please try using the original file path.

vcf.fn <- "/Users/Desktop/batch_1.vcf"
seqarray_test1 <- seqVCF2GDS(vcf.fn, "mangrove.gds")
ADD COMMENTlink written 8 months ago by Stephanie M. Gogarten600
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