Seq Array converting VCF to GDS using seqVCF2GDS, unable to find file problems with vcf.fn
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cav3gh • 0
@cav3gh-15680
Last seen 5.3 years ago

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 • 1.4k views
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zhengx ▴ 30
@zhengx-7950
Last seen 4.9 years ago
United States

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.

 

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@stephanie-m-gogarten-5121
Last seen 9 days ago
University of Washington

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")
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