Import VDJtools Clonotypes

The VDJtools Clonotypes format is a simple text file format of the VDJtools software package [Shugay et al., 2015].

To import this format, use the Standard Import tool:

        Import (Image Next_Folder_16_n_p) | Standard Import (Image Next_Folder_16_n_p)

Select VDJtools Clonotypes (.txt) in the Force import as type menu of the dialog.

The file format is tab-separated. The first line of the file must start with a '#' and describe the contents of the columns. An example first line is:

#count freq cdr3nt cdr3aa v d j VEnd DStart DEnd JStart

The following named columns must be present in the file: "count", "freq", "cdr3nt", "cdr3aa", "v", "j". All other columns are ignored during import.

For non-coding CDR3 sequences, the "cdr3aa" column may represent an incomplete codon using either "~" or "_".

The importer produces a TCR clonotypes element (Image tcr_table_16_n_p) and / or a BCR clonotypes element (Image bcr_table_16_n_p) (see Clonotypes), depending on the data found in the file.

Note that:

  • It is possible to export Immune Repertoires (Image tcr_table_16_n_p) to VDJ Tools txt format, share the results with collaborators, and re-import.
  • If the license allows use within your organization, VDJtools can be used to convert several other clonotype formats into this format.