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I am reading 2 vcf files in to R. They load fine (I have used 3 different methods to do this (read.vcf, readVCF, and fread) and all are fine) however when I go on to try and do anything with 1 of the vcf files, the msg reads:

Error in unlist_as_integer(x@subscript) : object 'fancy_mseq' not found

Error in h(simpleError(msg, call)) :
  error in evaluating the argument 'x' in selecting a method for function 'from': object 'fancy_mseq' not found

Usually I just google error msgs but I can not find anything online about this. Does anyone have any idea what could be causing this error message? Whilst it's hard to be 100% sure because of the vcf format, I can't see anything wrong with the file when I call str(), head() or any other ways of looking at the data.

Thank you!

ayeepi
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    I'm a little unclear on where this error is occurring could you share the code you are using to read the file and what you are doing when this error is produced? Also which packages the vcf reading functions are coming from would be helpful. – Richard J. Acton Nov 24 '21 at 19:33

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