CODEWITHSUNDEEP
command-linebioinformaticsvcf-variant-call-format
tacos
tacos

Reputation: 11

Having trouble uploading .vcf file into plink

I am quite new to coding and using plink and currently having problems trying to upload my vcf file into the plink command prompt.

I typed:

plink --vcf [PD630.vcf]

But got this error:

Error: Failed to open [PD630.vcf]. (--vcf expects complete file name; did you forget the .vcf at the end?)

However, I have already typed the complete and accurate file name into the brackets multiple times.

Upvotes: 1

Views: 731

Answers (1)

IMSoP
IMSoP

Reputation: 97718

I think you have taken the usage instructions too literally.

It is common when writing out command-line parameters to use square brackets to represent an optional argument, so --vcf [filename] would mean "the --vcf switch can optionally be followed by a filename". The square brackets don't need to be typed literally, and typing them will make the program look for a file with those brackets in its name.

So instead of plink --vcf [filename.vcf] you probably want just plink --vcf filename.vcf.

Upvotes: 1

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