title: Error when converting .gprobs files from Impute2 to PLINK format
body: <p>I have a set of .gprobs files that I need to import into Plink. However, I keep getting the same error -- a problem in a specific line, even after I removed that line and the lines around it.</p>
  
  <p>The data: I concatenated all 22 chromosome .gprobs files. To do so, I did replace the '---' at the beginning of the individual .gprobs files with the corresponding chromosome number (so now each line starts CHR SNP BP A1 A2...) . I also removed the SNPs that weren't imputed well (INFO scores below 0.7)</p>
  
  <p>Code:</p>
  
  <pre><code>plink --gen data_chrALL.gprobs_chrcol_below0.7inforemoved --sample data_chr1.sample --out data_chrALL.gprobs_plink
  </code></pre>
  
  <p>The error message:</p>
  
  <pre><code>--data: 13404k variants converted.Error: Line 13404781 of .gen file has fewer tokens than expected.
  </code></pre>
  
  <p>As I said above, I removed that specific line and reran it, and got the same exact error message. I tried removing the lines above and below (in case the numbering was off by a header or something?) but again, same exact error.</p>
  
  <p>Any thoughts or suggestions would be greatly appreciated!!! I'm not sure if this is the best place to post this, but I'm in desperate need of help.</p>