`mixcr extend`

Imputes germline sequences to the uncovered edges of CDR3, if corresponding V or J gene for is uniquely determined (e.g. from the second mate of a read pair).

This procedure is typically used as a part of non-targeted RNA-Seq analysis pipeline for T-cells, to recover some of useful TCRs. It is not safe to use it for IGs, because of hypermutations. Tor TCRs which have relatively conservative sequence near conserved Cys and Phe/Trp, it can reconstruct additional clonotypes with relatively small chance to introduce false ones. Default parameters are specifically optimized to show zero false-positive rate. By default mixcr extend acts only on TCR sequences.

Command line options

mixcr extend 
    [--v-anchor <anchor_point>] 
    [--j-anchor <anchor_point>] 
    [--min-v-score <n>] 
    [--min-j-score <n>] 
    [--chains <chains>] 
    [--quality <n>] 
    [--report <path>] 
    [--json-report <path>] 
    [--threads <n>] 
    [--force-overwrite] 
    [--no-warnings] 
    [--verbose] 
    [--help]
    data.(vdjca|clns|clna) extendeed.(vdjca|clns|clna)

The command takes alignments (.vdjca) or clones (.clnx) file as input and produces the same format as output. Additionally, it produces a comprehensive report.

Basic command line options are:

data.(vdjca|clns|clna): Path to input file.
extendeed.(vdjca|clns|clna): Path where to write output. Will have the same file type.
--v-anchor <anchor_point>: V extension anchor point. Default value determined by the preset.
--j-anchor <anchor_point>: J extension anchor point. Default value determined by the preset.
--min-v-score <n>: Minimal V hit score to perform left extension. Default value determined by the preset.
--min-j-score <n>: Minimal J hit score to perform right extension. Default value determined by the preset.
-c, --chains <chains>: Apply procedure only to alignments with specific immunological-receptor chains. Default: TCR
-q, --quality <n>: Quality score value to assign imputed sequences. Default: 30
-r, --report <path>: Report file (human readable version, see -j / --json-report for machine readable report).
-j, --json-report <path>: JSON formatted report file.
-t, --threads <n>: Processing threads
-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.