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mixcr exportAirr

Exports alignments from .vdjca file or clonotypes from .clns/.clna files in AIRR format.

mixcr exportAirr 
    [--target <n>] 
    [--imgt-gaps] 
    [--from-alignment] 
    [--limit <n>] 
    [--force-overwrite] 
    [--no-warnings] 
    [--verbose] 
    [--help]
    input.(vdjca|clna|clns) [output.tsv]

Command line options:

input_file.(vdjca|clna|clns)
Path to input file
[output.tsv]
Path where to write export. Will write to output if omitted.
-t, --target <n>
Target id (use -1 to export from the target containing CDR3).
-g, --imgt-gaps
If this option is specified, alignment fields will be padded with IMGT-style gaps.
-a, --from-alignment
Get fields like fwr1, cdr2, etc.. from alignment.
-n, --limit <n>
Limit number of filtered alignments; no more than N alignments will be outputted
-f, --force-overwrite
Force overwrite of output file(s).
-nw, --no-warnings
Suppress all warning messages.
--verbose
Verbose warning messages.
-h, --help
Show this help message and exit.

For some downstream analysis tools one also should prepare gapped reference using --imgt option for repseqio:

# from built-in MiXCR reference
> repseqio fasta --imgt \
    --species hs \
    -g 'VRegion' \
    default \
    vregion_gapped.fasta

# from IMGT reference
> repseqio fasta --imgt \
    --species hs \
    -g 'VRegion' \
    imgt.202209-1.sv7.json.gz \
    vregion_gapped.fasta