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>

Index of source sequence that was used to build clone/alignment (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 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