Import/Export VDJtools Clonotypes
The VDJtools format is a simple clonotype 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 (
) and BCR clonotypes (
) (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. |
Import
To import this format, use the Standard Import tool:
Import (
) | Standard Import ()
Select VDJtools Clonotypes (.txt) in the Force import as type menu of the dialog.
The following columns are read from the file:
- "count", "freq", "cdr3nt", and "cdr3aa". These must be present in the file.
- "v", "d", "j", and "c". At least one of these must be present in the file.
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.
Export
To export clonotypes to a text file, launch the Export tool by clicking on the Export button in the toolbar, or going to the File menu and choosing Export.... To easily locate the "VDJ Tools" exporter, type "vdj" into the search field at the top of the tool.