Import/Export VDJtools Clonotypes

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

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

Import and export from and to this format is supported for both TCR clonotypes (Image tcr_table_16_n_p) and BCR clonotypes (Image bcr_table_16_n_p) (see Clonotypes).

Note that, if the license allows use within your organization, VDJtools can be used to convert several other clonotype formats into this format.


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 columns "count", "freq", "cdr3nt", "cdr3aa", "v", and "j" must be present in the file, while the "d" column is optional. 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 and / or BCR clonotypes element, depending on the data found in the file.


To launch the export toolbox use the menu or click the Export button in the top left corner of the CLC Workbench. Start typing "vdj" to identify the "VDJ Tools txt" exporter.