Convert row to column basis on character

static void Main()
    {
        string[] lines = File.ReadAllLines("D:\\InputFile.txt");
        List<string> list = new List<string>();

        //Start a string to hold the current line...
        string currentLine = "";

        foreach (var item in lines)
        {
            if (item == "~")
            {
                //Add the current line to the list when '~' sign is found...
                list.Add(currentLine);

                //Reset your current line for the next set of values...
                currentLine = "";
            }
            else
            {
                //Concatenate the current item to your current line...
                currentLine += item;
            }
        }

        //Add the last line to the list (assuming the file doesn't end with '~')...
        list.Add(currentLine);

        //Print your result...
        list.ForEach(i => Console.WriteLine(i));
    }

It seems to me that you can do the required formatting in one line of code.

List<string> lines = ["~", "A", "B", "~", "C", "D","~","E","F"];
string[] formattedLines = string.Join('~', lines).Trim('~').Split("~~~");

A call to string.Join('~', lines) concatenates the lines into a single line where each line forms a substring separated by a '~' . At this stage the result is '~~A~B~~~C~D~~~E~F'.So all that is needed now is to Trim the two '~' from the start of the string and then split on '~~~'.

      string text = 
@"
~
A
B
~
C
D
" ;

      foreach 
      ( 
        string s 
      in 
        Rearranger
        (
          new System.Text.RegularExpressions.Regex 
          ( 
            @"(~)\r\n(\S+)\r\n(\S+)" 
          , 
            System.Text.RegularExpressions.RegexOptions.Compiled 
          ) 
        ,
          new int[] { 2 , 1 , 3 }
        ,
          text
        ) 
      )
      {
        System.Console.WriteLine ( s ) ;
      }

private static readonly System.Text.StringBuilder buffer =
  new System.Text.StringBuilder() ;

private static System.Collections.Generic.IEnumerable<string>
Rearranger
(
  System.Text.RegularExpressions.Regex Splitter
,
  int[]                                GroupOrder
,
  string                               Input
)
{
  System.Text.RegularExpressions.MatchCollection mat = Splitter.Matches ( Input ) ;

  lock ( buffer )
  {
    for ( int i = 0 ; i < mat.Count ; i++ )
    {
      buffer.Length = 0 ;

      for ( int j = 0 ; j < GroupOrder.Length ; j++ )
      {
        buffer.Append ( mat [ i ].Groups [ GroupOrder [ j ] ].Value ) ;
      }

      yield return ( buffer.ToString() ) ;
    }
  }

  yield break ;
}