Mix-in options list

MiXCR provides a set of mix-in options allowing to configure analysis pipeline using high-level primitives.

Alignment mix-in options

The following mix-in options configure align step.

--species: Species
Species (organism), as specified in library file or taxon id.

Possible values: hs, HomoSapiens, musmusculus, mmu, hsa, 9606, 10090 etc.

--library: Specify reference V-, D-, J-, C- gene segment library.
--split-by-sample: Split output alignments files by sample.
--dont-split-by-sample: Don't split output alignments files by sample.
--infer-sample-table: Infer sample table (supports only sample tags derived from file names).
--sample-sheet <sample_sheet.tsv>: Loads sample table from a tab separated file.
--dna: Material type
For DNA starting material. Setups V gene feature to align to VGeneWithP (full intron) and also instructs MiXCR to skip C gene alignment since it is too far from CDR3 in DNA data.
--rna: Material type
For RNA starting material; setups VTranscriptWithP (full exon) gene feature to align for V gene and CExon1 for C gene.
--floating-left-alignment-boundary [<anchor_point>]: Left alignment boundary
Configures aligners to use semi-local alignment at reads 5'-end. Typically used with V gene single primer / multiplex protocols, or if there are non-trimmed adapter sequences at 5'-end. Optional anchor point may be specified to instruct MiXCR where the primer is located and strip V feature to align accordingly, resulting in a more precise alignments.
--rigid-left-alignment-boundary [<anchor_point>]: Left alignment boundary
Configures aligners to use global alignment at reads 5'-end. Typically used for 5'RACE with template switch oligo or a like protocols. Optional anchor point may be specified to instruct MiXCR how to strip V feature to align.
--floating-right-alignment-boundary (<gene_type>|<anchor_point>): Right alignment boundary
Configures aligners to use semi-local alignment at reads 3'-end. Typically used with J or C gene single primer / multiplex protocols, or if there are non-trimmed adapter sequences at 3'-end. Requires either gene type (J for J primers / C for C primers) or anchor point to be specified. In latter case MiXCR will additionally strip feature to align accordingly.
--rigid-right-alignment-boundary [(<gene_type>|<anchor_point>)]: Right alignment boundary
Configures aligners to use global alignment at reads 3'-end. Typically used for J-C intron single primer / multiplex protocols. Optional gene type (J for J primers / C for C primers) or anchor point may be specified to instruct MiXCR where how to strip J or C feature to align.
--tag-pattern: Tag pattern
Specify tag pattern for barcoded data.
--keep-non-CDR3-alignments: Debug
Preserve alignments that do not cover CDR3 region or cover it only partially in the .vdjca file.
--drop-non-CDR3-alignments: Debug
Drop all alignments that do not cover CDR3 region or cover it only partially.
--limit-input: Debug
Maximal number of reads to process.

Refine tags and sort mix-in options

The following mix-in options configure refineTagsAndSort step.

--set-whitelist <key=value>

Sets the whitelist for a specific tag to guide the tag refinement procedure. Usage:

--set-whitelist CELL=preset:737K-august-2016

or

--set-whitelist UMI=file:my_umi_whitelist.txt

--reset-whitelist tag

Resets the whitelist for a specific tag so that unguided refinement procedure will be applied for it. Usage:

Clonotype assembly mix-in options

The following mix-in options configure assemble step.

--assemble-clonotypes-by <gene_features>: Specify gene features used to assemble clonotypes. One may specify any custom gene region (e.g. FR3+CDR3); target clonal sequence can even be disjoint. Note that assemblingFeatures must cover CDR3.
--split-clones-by <gene_type>: Clones with equal clonal sequence but different gene will not be merged.
--dont-split-clones-by <gene_type>: Clones with equal clonal sequence but different gene will be merged into single clone.

Contig assembly mix-in options

The following mix-in options configure assembleContigs step.

--assemble-contigs-by <gene_features>: Selects the region of interest for the action. Clones will be separated if inconsistent nucleotides will be detected in the region, assembling procedure will be limited to the region, and only clonotypes that fully cover the region will be outputted, others will be filtered out.

Export mix-in options

The following mix-in options configure clonotype export step.

--impute-germline-on-export: Export nucleotide sequences using letters from germline (marked lowercase) for uncovered regions.
--dont-impute-germline-on-export: Export nucleotide sequences only from covered region.
--prepend-export-clones-field <field> [<param>...]: Add clones export column before other columns. First param is field name as it is in exportClones command, left params are params of the field
--append-export-clones-field <field> [<param>...]: Add clones export column after other columns. First param is field name as it is in exportClones command, left params are params of the field
--prepend-export-alignments-field <field> [<param>...]: Add clones export column before other columns. First param is field name as it is in exportAlignments command, left params are params of the field
--append-export-alignments-field <field> [<param>...]: Add clones export column after other columns. First param is field name as it is in exportAlignments command, left params are params of the field
--add-export-clone-table-splitting <(geneLabel|tag):key>: Add key to split output files with clone tables.
--reset-export-clone-table-splitting: Reset all file splitting for output clone tables.
--add-export-clone-grouping <(geneLabel|tag):key>: Add key to group clones in the output clone tables.
--reset-export-clone-grouping: Reset all clone grouping in the output clone tables.
--export-productive-clones-only: Export only productive clonotypes.

Pipeline configuration mix-ins

The following mix-in options configure general pipeline execution.

--add-step <step_name>: Add execution step.
--remove-step <step_name>: Remove execution step.