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.
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.