Multiple annotation tools can be utilized to evaluate the sequences and produce rearrangements: MiXCR is the most common tool for TCR sequences, while IMGT and IgBlast are preferred for BCR sequences. How the annotation tool was run, including the parameters used for the annotation, should be denoted in the metadata file. The most comprehensive mechanism for this would be to record the actual command line that was used to run the tool in the metadata file. The most complete germline database for both BCR and TCR sequences (for humans and mice) is IMGT, so even when utilizing MiXCR and IgBlast, the reference library for genes should be IMGT. If you use a custom germline database, it is critical that you identify the germline database and how it differs from the IMGT germline database in the Metadata CSV file so that researchers can assess whether it makes sense to compare rearrangements that are annotated with different germlines.
If the previous steps were followed correctly, sequences should be prepared for annotation and can be run directly in the programs. Of course, documentation for each program should be referred to before annotation to ensure that the ideal information is captured with their parameters.