Export SHM Trees

MiXCR provides functions for export SHM Trees, SHM Trees with all nodes in a tab-delimited way. Additionally, SHM trees may be export in NEWICK format.

.shmt produced by findShmTrees and holds SHM trees and clonotypes that included in trees.

SHM trees tables

mixcr exportShmTrees [-f]
    [--filter-min-nodes <n>] 
    [--filter-min-height <n>] 
    [--ids <id>[,<id>...]]...
    [--chains <chains>] 
    [--preset <preset>]
    [--preset-file <file>]
    [--no-header]
    [--not-covered-as-empty] 
    [<exportField>]...
    [--force-overwrite] 
    [--no-warnings] 
    [--verbose] 
    [--help] 
    [[--filter-in-feature <gene_feature>] [--pattern-max-errors <n>] (--filter-aa-pattern <pattern> | --filter-nt-pattern <pattern>)] 
    trees.shmt [trees.tsv]

Exports tab-delimited info from .shmt file for found SHM trees, without information about each node.

Command line options:

trees.shmt

Input file produced by 'findShmTrees' command.

[trees.tsv]

Path to output table. Print in stdout if omitted.

--filter-min-nodes <n>

Minimal number of nodes in tree

--filter-min-height <n>

Minimal height of the tree

--ids <id>[,<id>...]

Filter specific trees by id

--chains <chains>

Export only trees that contains clones with specific chain (e.g. TRA or IGH).

-p, --preset <preset>

Specify preset of export fields (possible values: 'full', 'min'; 'full' by default)

-pf, --preset-file <presetFile>

Specify preset file of export fields

--no-header

Don't print column names

--not-covered-as-empty

Export not covered regions as empty text.

-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.

<exportField>

A list of export fields

Filter by pattern options:

--filter-in-feature <gene_feature>

Match pattern inside specified gene feature. Default: CDR3

--pattern-max-errors <n>

Max allowed subs & indels. Default: 0

--filter-aa-pattern <pattern>

Filter specific trees by aa pattern.

--filter-nt-pattern <pattern>

Filter specific trees by nt pattern.

SHM trees with nodes tables

mixcr exportShmTreesWithNodes [-f]
    [--only-observed] 
    [--filter-min-nodes <n>] 
    [--filter-min-height <n>] 
    [--ids <id>[,<id>...]]... 
    [--chains <chains>] 
    [--preset <preset>] 
    [--preset-file <presetFile>] 
    [--no-header]
    [--not-covered-as-empty]
    [<exportField>]...
    [--force-overwrite] 
    [--no-warnings] 
    [--verbose]  
    [--help] 
    [[--filter-in-feature <gene_feature>] [--pattern-max-errors <n>] (--filter-aa-pattern <pattern> | --filter-nt-pattern <pattern>)] 
    trees.shmt [trees.tsv]

Exports tab-delimited info from .shmt file for every node of SHM trees.

Command line options:

trees.shmt

Input file produced by 'findShmTrees' command.

[trees.tsv]

Path where to write output export table. Print in stdout if omitted.

--only-observed

Exclude nodes that was reconstructed by algorithm

--filter-min-nodes <n>

Minimal number of nodes in tree

--filter-min-height <n>

Minimal height of the tree

--ids <id>[,<id>...]

Filter specific trees by id

--chains <chains>

Export only trees that contains clones with specific chain (e.g. TRA or IGH).

-p, --preset <preset>

Specify preset of export fields (possible values: 'min', 'full'; 'full' by default)

-pf, --preset-file <presetFile>

Specify preset file of export fields

--no-header

Don't print column names

--not-covered-as-empty

Export not covered regions as empty text.

-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.

<exportField>

A list of export fields

Filter by pattern options:

--filter-in-feature <gene_feature>

Match pattern inside specified gene feature. Default: CDR3

--pattern-max-errors <n>

Max allowed subs & indels. Default: 0

--filter-aa-pattern <pattern>

Filter specific trees by aa pattern.

--filter-nt-pattern <pattern>

Filter specific trees by nt pattern.

NEWICK

mixcr exportShmTreesNewick 
    [--filter-min-nodes <n>] 
    [--filter-min-height <n>] 
    [--ids <id>[,<id>...]]... 
    [--chains <chains>]
    [--force-overwrite] 
    [--no-warnings] 
    [--verbose] 
    [--help] 
    [[--filter-in-feature <gene_feature>] [--pattern-max-errors <n>] (--filter-aa-pattern <pattern> | --filter-nt-pattern <pattern>)] 
    trees.shmt outputDir

Export SHM trees in NEWICK format.

NEWICK will be printed with distances, leafs. As content nodeId will be printed.

Command line options:

trees.shmt

Input file produced by 'findShmTrees' command.

outputDir

Output directory to write newick files. Separate file for every tree will be created

--filter-min-nodes <n>

Minimal number of nodes in tree

--filter-min-height <n>

Minimal height of the tree

--ids <id>[,<id>...]

Filter specific trees by id

--chains <chains>

Export only trees that contains clones with specific chain (e.g. TRA or IGH).

-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.

Filter by pattern options:

--filter-in-feature <gene_feature>

Match pattern inside specified gene feature. Default: CDR3

--pattern-max-errors <n>

Max allowed subs & indels. Default: 0

--filter-aa-pattern <pattern>

Filter specific trees by aa pattern.

--filter-nt-pattern <pattern>

Filter specific trees by nt pattern.

Examples

For convenience, MiXCR provides two predefined sets of fields for exporting SHM trees: min (will export minimal required information about tree or tree nodes) and full (used by default); one can use these sets by specifying the --preset option:

> mixcr exportShmTrees --preset min trees.shmt trees.tsv

One can add additional columns to the preset in the following way:

> mixcr exportShmTreesWithNodes --preset min -qFeature CDR2 trees.shmt trees_with_nodes.tsv

One can also put all specify export fields in a separate file

> cat myFields.txt
-vHits
-dHits
-nFeature CDR3

> mixcr exportShmTreesWithNodes --preset-file myFields.txt trees.shmt trees_with_nodes.tsv

Export fields

SHM tree-specific fields

The following fields are available for both exportShmTrees and exportShmTreesWithNodes:

-treeId

SHM tree id

-numberOfClonesInTree

Number of uniq clones in the SHM tree

-totalReadsCountInTree

Total sum of read counts of clones in the SHM tree

-totalUniqueTagCountInTree <(Molecule|Cell|Sample)>

Total count of unique tags in the SHM tree with specified type

The following fields are only available for exportShmTrees:

-vHit

Export best V hit

-jHit

Export best J hit

-nFeature <gene_feature> [(germline|mrca|parent)]

Export nucleotide sequence of specified gene feature of specified node type. If second arg is omitted, then feature will be printed for current node. Otherwise - for corresponding parent, germline or mrca.

-allNFeatures [(germline|mrca|parent)]

Export nucleotide sequences for all covered gene features. If first arg is omitted, then feature will be printed for current node. Otherwise - for corresponding parent, germline or mrca.

-aaFeature <gene_feature> [(germline|mrca|parent)]

Export amino acid sequence of specified gene feature of specified node type. If second arg is omitted, then feature will be printed for current node. Otherwise - for corresponding parent, germline or mrca.

-allAAFeatures [(germline|mrca|parent)]

Export nucleotide sequences for all covered gene features. If first arg is omitted, then feature will be printed for current node. Otherwise - for corresponding parent, germline or mrca.

SHM tree node-specific fields

The following fields are available only for exportShmTreesWithNodes:

-nodeId

Node id in SHM tree

-isObserved

Is node have clones. All other nodes are reconstructed by algorithm

-parentId

Parent node id in SHM tree

-distance <(germline|mrca|parent)>

Distance from another node in number of mutations.

-fileName

Name of clns file with sample

-nFeature <gene_feature> [(germline|mrca|parent)]

Export nucleotide sequence of specified gene feature. If second arg is omitted, then feature will be printed for a current node. Otherwise - for corresponding parent, germline or mrca.

-allNFeatures [(germline|mrca|parent)]

Export nucleotide sequences for all covered gene features. If first arg is omitted, then feature will be printed for a current node. Otherwise - for corresponding parent, germline or mrca.

-aaFeature <gene_feature> [(germline|mrca|parent)]

Export amino acid sequence of specified gene feature. If second arg is omitted, then feature will be printed for a current node. Otherwise - for corresponding parent, germline or mrca.

-allAAFeatures [(germline|mrca|parent)]

Export amino acid sequences for all covered gene features. If first arg is omitted, then feature will be printed for a current node. Otherwise - for corresponding parent, germline or mrca.

-nLength <gene_feature> [(germline|mrca|parent)]

Export length of specified gene feature in nucleotides. If second arg is omitted, then feature length will be printed for a current node. Otherwise - for corresponding parent, germline or mrca.

-allNLength [(germline|mrca|parent)]

Export lengths for all covered gene features in nucleotides. If first arg is omitted, then feature will be printed for a current node. Otherwise - for corresponding parent, germline or mrca.

-aaLength <gene_feature> [(germline|mrca|parent)]

Export length of specified gene feature in amino acids. If second arg is omitted, then feature length will be printed for a current node. Otherwise - for corresponding parent, germline or mrca. If second option is germline then corresponding top genes will be counted excluding CDR3 (VJJunction germline is unknown). It's recommended to run findAlleles before exporting -aaLength <gene_feature> germline because otherwise germline sequence will not incorporate allelic mutations. (only for nodes with clones)

-allAALength [<(germline|mrca|parent)>]

Export lengths for all covered gene features in amino acids. If the first arg is omitted, then feature will be printed for a current node. Otherwise - for corresponding parent, germline or mrca.

-nMutations <gene_feature> [(germline|mrca|parent)] [(substitutions|indels|inserts|deletions)]

Extract nucleotide mutations from specific node for specific gene feature. If the second arg is omitted, then mutations will be calculated from germline. Otherwise - for corresponding parent, germline or mrca. By default, exports all types of mutations. One can specify a mutation type using the third arg.

-allNMutations [(germline|mrca|parent)] [(substitutions|indels|inserts|deletions)]

Extract nucleotide mutations from specific node for all covered gene features. If the first arg is omitted, then mutations will be calculated from germline. Otherwise - for corresponding parent, germline or mrca. By default, exports all types of mutations. One can specify a mutation type using the third arg.

-nMutationsRelative <gene_feature> <relative_to_gene_feature> [(germline|mrca|parent)] [(substitutions|indels|inserts|deletions)]

Extract nucleotide mutations from specific node for specific gene feature relative to another feature. If the third arg is omitted, mutations will be calculated from the germline. Otherwise - for corresponding parent, germline or mrca. By default, exports all types of mutations. One can specify a mutation type using the fourth arg.

-aaMutations <gene_feature> [(germline|mrca|parent)] [(substitutions|indels|inserts|deletions)]

Extract amino acid mutations from specific node for specific gene feature. If the second arg is omitted, mutations will be calculated from the germline. Otherwise - for corresponding parent, germline or mrca. By default, exports all types of mutations. One can specify a mutation type using the third arg.

-allAAMutations [(germline|mrca|parent)] [(substitutions|indels|inserts|deletions)]

Extract amino acid mutations from specific node for all covered gene features. If the first arg is omitted, then mutations will be calculated from germline. Otherwise - for corresponding parent, germline or mrca. By default, exports all types of mutations. One can specify a mutation type using the third arg.

-aaMutationsRelative <gene_feature> <relative_to_gene_feature> [(germline|mrca|parent)] [(substitutions|indels|inserts|deletions)]

Extract amino acid mutations from specific node for specific gene feature relative to another feature. If the third arg is omitted, mutations will be calculated from the germline. Otherwise - for corresponding parent, germline or mrca. By default, exports all types of mutations. One can specify a mutation type using the fourth arg.

-mutationsDetailed <gene_feature> [(germline|mrca|parent)]

Detailed list of nucleotide and corresponding amino acid mutations from specific node. Format <nt_mutation>:<aa_mutation_individual>:<aa_mutation_cumulative>, where <aa_mutation_individual> is an expected amino acid mutation given no other mutations have occurred, and <aa_mutation_cumulative> amino acid mutation is the observed amino acid mutation combining effect from all others. If the second arg is omitted, mutations will be calculated from the germline. Otherwise - for corresponding parent, germline or mrca.

-allMutationsDetailed [(germline|mrca|parent)]

Detailed list of nucleotide and corresponding amino acid mutations from specific node for all covered gene features. If the first arg is omitted, then mutations will be calculated from germline. Otherwise - for corresponding parent, germline or mrca.

-mutationsDetailedRelative <gene_feature> <relative_to_gene_feature> [(germline|mrca|parent)]

Detailed list of nucleotide and corresponding amino acid mutations written, positions relative to specified gene feature. Format ::, where is an expected amino acid mutation given no other mutations have occurred, and amino acid mutation is the observed amino acid mutation combining effect from all others. WARNING: format may change in following versions.

-nMutationsCount [<gene_feature>] [(germline|mrca|parent)] [(substitutions|indels|inserts|deletions)]

Number of nucleotide mutations. By default, will be used all covered features. Resolutions of wildcards in VJJunction are excluded from calculation. If second arg is omitted, then mutations will be calculated from germline. Otherwise - for corresponding parent, germline or mrca.

-allNMutationsCount [(germline|mrca|parent)] [(substitutions|indels|inserts|deletions)]

Number of nucleotide mutations for all covered gene features. Resolutions of wildcards in VJJunction are excluded from calculation. If first arg is omitted, then mutations will be calculated from germline. Otherwise - for corresponding parent, germline or mrca.

-aaMutationsCount [<gene_feature>] [(germline|mrca|parent)] [(substitutions|indels|inserts|deletions)]

Number of amino acid mutations. By default, will be used all covered features. Resolutions of wildcards in CDR3 are excluded from calculation. If second arg is omitted, then mutations will be calculated from the germline. Otherwise - for corresponding parent, germline or mrca.

-allAAMutationsCount [(germline|mrca|parent)] [(substitutions|indels|inserts|deletions)]

Number of amino acid mutations for all covered gene features. Resolutions of wildcards in CDR3 are excluded from calculation. If first arg is omitted, then mutations will be calculated from germline. Otherwise - for corresponding parent, germline or mrca.

-nMutationRate [<gene_feature>] [(substitutions|indels|inserts|deletions)]

Number of nucleotide mutations from germline divided by target sequence size. By default, will be used all covered features. Resolutions of wildcards in VJJunction are excluded from calculation.

-aaMutationRate [<gene_feature>] [(substitutions|indels|inserts|deletions)]

Number of amino acid mutations from germline divided by target sequence size. By default, will be used all covered features. Resolutions of wildcards in CDR3 are excluded from calculation.

-biochemicalProperty <gene_feature> <property> [(germline|mrca|parent)]

Biochemical property of specified gene feature normalized by AA sequence size. Possible values: Hydropathy, Charge, Polarity, Volume, Strength, MjEnergy, Kf1, Kf2, Kf3, Kf4, Kf5, Kf6, Kf7, Kf8, Kf9, Kf10, Rim, Surface, Turn, Alpha, Beta, Core, Disorder, N2Strength, N2Hydrophobicity, N2Volume, N2Surface

-baseBiochemicalProperties <gene_feature> [(germline|mrca|parent)]

Base biochemical properties of specified gene feature normalized by AA sequence size: N2Strength, N2Hydrophobicity, N2Surface, N2Volume, Charge

The following fields are available only for exportShmTreesWithNodes on nodes with clones:

-targets

Export number of targets

-dHit

Export best D hit

-cHit

Export best C hit

-vGene

Export best V hit gene name (e.g. TRBV12-3 for TRBV12-3*00)

-dGene

Export best D hit gene name (e.g. TRBV12-3 for TRBV12-3*00)

-jGene

Export best J hit gene name (e.g. TRBV12-3 for TRBV12-3*00)

-cGene

Export best C hit gene name (e.g. TRBV12-3 for TRBV12-3*00)

-vFamily

Export best V hit family name (e.g. TRBV12 for TRBV12-3*00)

-dFamily

Export best D hit family name (e.g. TRBV12 for TRBV12-3*00)

-jFamily

Export best J hit family name (e.g. TRBV12 for TRBV12-3*00)

-cFamily

Export best C hit family name (e.g. TRBV12 for TRBV12-3*00)

-vHitScore

Export score for best V hit

-dHitScore

Export score for best D hit

-jHitScore

Export score for best J hit

-cHitScore

Export score for best C hit

-vHitsWithScore

Export all V hits with score

-dHitsWithScore

Export all D hits with score

-jHitsWithScore

Export all J hits with score

-cHitsWithScore

Export all C hits with score

-vHits

Export all V hits

-dHits

Export all D hits

-jHits

Export all J hits

-cHits

Export all C hits

-vGenes

Export all V gene names (e.g. TRBV12-3 for TRBV12-3*00)

-dGenes

Export all D gene names (e.g. TRBV12-3 for TRBV12-3*00)

-jGenes

Export all J gene names (e.g. TRBV12-3 for TRBV12-3*00)

-cGenes

Export all C gene names (e.g. TRBV12-3 for TRBV12-3*00)

-vFamilies

Export all V gene family anmes (e.g. TRBV12 for TRBV12-3*00)

-dFamilies

Export all D gene family anmes (e.g. TRBV12 for TRBV12-3*00)

-jFamilies

Export all J gene family anmes (e.g. TRBV12 for TRBV12-3*00)

-cFamilies

Export all C gene family anmes (e.g. TRBV12 for TRBV12-3*00)

-vAlignment

Export best V alignment

-dAlignment

Export best D alignment

-jAlignment

Export best J alignment

-cAlignment

Export best C alignment

-vAlignments

Export all V alignments

-dAlignments

Export all D alignments

-jAlignments

Export all J alignments

-cAlignments

Export all C alignments

-qFeature <gene_feature>

Export quality string of specified gene feature

-nFeatureImputed <gene_feature>

Export nucleotide sequence of specified gene feature using letters from germline (marked lowercase) for uncovered regions

-allNFeaturesImputed [<from_reference_point> <to_reference_point>]

Export nucleotide sequence using letters from germline (marked lowercase) for uncovered regions for all gene features between specified reference points (in separate columns).

For example, -allNFeaturesImputed FR3Begin FR4End will export -nFeatureImputed FR3, -nFeatureImputed CDR3, -nFeatureImputed FR4.

By default, boundaries will be got from analysis parameters if possible or FR1Begin FR4End otherwise.

-aaFeatureImputed <gene_feature>

Export amino acid sequence of specified gene feature using letters from germline (marked lowercase) for uncovered regions

-allAAFeaturesImputed [<from_reference_point> <to_reference_point>]

Export amino acid sequence using letters from germline (marked lowercase) for uncovered regions for all gene features between specified reference points (in separate columns).

For example, -allAAFeaturesImputed FR3Begin FR4End will export -aaFeatureImputed FR3, -aaFeatureImputed CDR3, -aaFeatureImputed FR4.

By default, boundaries will be got from analysis parameters if possible or FR1Begin FR4End otherwise.

-minFeatureQuality <gene_feature>

Export minimal quality of specified gene feature

-allMinFeaturesQuality [<from_reference_point> <to_reference_point>]

Export minimal quality for all gene features between specified reference points (in separate columns).

For example, -allMinFeaturesQuality FR3Begin FR4End will export -minFeatureQuality FR3, -minFeatureQuality CDR3, -minFeatureQuality FR4.

By default, boundaries will be got from analysis parameters if possible or FR1Begin FR4End otherwise.

-allNFeaturesWithMinQuality [<from_reference_point> <to_reference_point>]

Export nucleotide sequences and minimal quality for all gene features between specified reference points (in separate columns).

For example, -allNFeaturesWithMinQuality FR3Begin FR4End will export -nFeature FR3, -minFeatureQuality FR3, -nFeature CDR3, -minFeatureQuality CDR3, -nFeature FR4, -minFeatureQuality FR4.

By default, boundaries will be got from analysis parameters if possible or FR1Begin FR4End otherwise.

-allNFeaturesImputedWithMinQuality [<from_reference_point> <to_reference_point>]

Export nucleotide sequences and minimal quality for all gene features between specified reference points (in separate columns).

For example, -allNFeaturesImputedWithMinQuality FR3Begin FR4End will export -nFeatureImputed FR3, -minFeatureQuality FR3, -nFeatureImputed CDR3, -minFeatureQuality CDR3, -nFeatureImputed FR4, -minFeatureQuality FR4.

By default, boundaries will be got from analysis parameters if possible or FR1Begin FR4End otherwise.

-avrgFeatureQuality <gene_feature>

Export average quality of specified gene feature

-allAvrgFeaturesQuality [<from_reference_point> <to_reference_point>]

Export average quality for all gene features between specified reference points (in separate columns).

For example, -allAvrgFeaturesQuality FR3Begin FR4End will export -avrgFeatureQuality FR3, -avrgFeatureQuality CDR3, -avrgFeatureQuality FR4.

By default, boundaries will be got from analysis parameters if possible or FR1Begin FR4End otherwise.

-positionInReferenceOf <reference_point>

Export position of specified reference point inside reference sequences (clonal sequence / read sequence).

-allPositionsInReference [<from_reference_point> <to_reference_point>]

Export position inside reference sequences (clonal sequence / read sequence) for all reference points between specified (in separate columns).

For example, -allPositionsInReference FR3Begin FR4End will export -positionInReferenceOf FR3Begin, -positionInReferenceOf CDR3Begin, -positionInReferenceOf CDR3End and -positionInReferenceOf FR4End.

By default, boundaries will be got from analysis parameters if possible or FR1Begin FR4End otherwise.

-positionOf <reference_point>

Export position of specified reference point inside target sequences (clonal sequence / read sequence).

-allPositions [<from_reference_point> <to_reference_point>]

Export position inside target sequences (clonal sequence / read sequence) for all reference points between specified (in separate columns).

For example, -allPositions FR3Begin FR4End will export -positionOf FR3Begin, -positionOf CDR3Begin, -positionOf CDR3End and -positionOf FR4End.

By default, boundaries will be got from analysis parameters if possible or FR1Begin FR4End otherwise.

-defaultAnchorPoints

Outputs a list of default reference points (like CDR2Begin, FR4End, etc. see documentation bellow for the full list and formatting)

-cloneId

Unique clone identifier

-readCount

Number of reads assigned to the clonotype

-readFraction

Fraction of reads assigned to the clonotype

-targetSequences

Export aligned sequences (targets), separated with comma

-targetQualities

Export aligned sequence (target) qualities, separated with comma

-vIdentityPercents

V alignment identity percents

-dIdentityPercents

D alignment identity percents

-jIdentityPercents

J alignment identity percents

-cIdentityPercents

C alignment identity percents

-vBestIdentityPercent

V best alignment identity percent

-dBestIdentityPercent

D best alignment identity percent

-jBestIdentityPercent

J best alignment identity percent

-cBestIdentityPercent

C best alignment identity percent

-chains

Chains

-isotype [(primary|subclass|auto)]

Export isotype for IGH chains if it's distinguishable. primary will resolve 'IgA', 'IgD', 'IgG', 'IgE', 'IgM'. subtype will try resolve isotypes like 'IgA1' or 'IgA2'. Default auto will automatically decide whether to resolve the primary or subtype isotype based on the level of detail distinguishable for each clone.

-geneLabel <label>

Export gene label (i.e. ReliableChain)

-tagCounts

All tags with counts

-tags <(Molecule|Cell|Sample)>

All tags values (i.e. CELL barcode or UMI sequence).

-uniqueTagCount <(Molecule|Cell|Sample)>

Unique tag count

Tag type will be used for filtering tags for export.

-uniqueTagFraction <(Molecule|Cell|Sample)>

Fraction of unique tags (UMI, CELL, etc.) the clone or alignment collected.

Tag type will be used for filtering tags for export.

-cellGroup

Cell group (for single cell analysis)