Usage: mixcr exportShmTrees [--filter-min-nodes <n>] [--filter-min-height <n>] [--ids <id>[,
                            <id>...]]... [--chains <chains>] [--preset <preset>] [--preset-file
                            <presetFile>] [--no-header] [--not-covered-as-empty] [-treeId]
                            [-subtreeId] [-numberOfClonesInTree [forChain]]...
                            [-numberOfNodesWithClones] [-totalReadsCountInTree [forChain]]...
                            [-totalUniqueTagCountInTree (Molecule|Cell|Sample) [forChain]]...
                            [-chains] [-treeHeight] [-vHit] [-jHit] [-vGene] [-jGene] [-vFamily]
                            [-jFamily] [-nFeature <gene_feature> (germline|mrca)]... [-allNFeatures
                            (germline|mrca)]... [-aaFeature <gene_feature> (germline|mrca)]...
                            [-allAAFeatures (germline|mrca)]... [-nFeatureImputed <gene_feature>
                            (germline|mrca)]... [-allNFeaturesImputed [<from_reference_point>
                            <to_reference_point>] (germline|mrca)]... [-aaFeatureImputed
                            <gene_feature> (germline|mrca)]... [-allAAFeaturesImputed
                            [<from_reference_point> <to_reference_point>] (germline|mrca)]...
                            [--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]
Export SHMTree as a table with a row for every SHM root in a table (single row if no single cell
data)
      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. IGK,
                               IGL or IGH).
  -p, --preset <preset>      Specify preset of export fields. Possible values: default,
                               defaultSingleCell, min.
      -pf, --preset-file <presetFile>
                             Specify preset file of export fields
      --no-header            Don't print first header line, print only data
      --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.
Filter by pattern
      --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.
Possible fields to export
      -treeId                SHM tree id
      -subtreeId             Id for different roots in single cell trees
      -numberOfClonesInTree [forChain]
                             Number of uniq clones in the SHM tree. If first parameter is
                               `forChain`, will calculate for this root, otherwise, for all roots
                               combined.
      -numberOfNodesWithClones
                             Number of nodes with clones, i.e. nodes with different clone
                               sequences. Other differences are not counting such as: isotypes,
                               sample, cell.
      -totalReadsCountInTree [forChain]
                             Total sum of read counts of clones in the SHM tree. If first parameter
                               is `forChain`, will calculate for this root, otherwise, for all
                               roots combined.
      -totalUniqueTagCountInTree (Molecule|Cell|Sample) [forChain]
                             Total count of unique tags in the SHM tree with specified type. If
                               first parameter is `forChain`, will calculate for this root,
                               otherwise, for all roots combined.
      -chains                Chain type of the tree
      -treeHeight            Height of the tree
      -vHit                  Export best V hit
      -jHit                  Export best J hit
      -vGene                 Export best V 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)
      -vFamily               Export best V hit family name (e.g. TRBV12 for TRBV12-3*00)
      -jFamily               Export best J hit family name (e.g. TRBV12 for TRBV12-3*00)
      -nFeature <gene_feature> (germline|mrca)
                             Export nucleotide sequence of specified gene feature of specified node
                               type.
      -allNFeatures (germline|mrca)
                             Export nucleotide sequences for all covered gene features.
      -aaFeature <gene_feature> (germline|mrca)
                             Export amino acid sequence of specified gene feature of specified node
                               type
      -allAAFeatures (germline|mrca)
                             Export nucleotide sequences for all covered gene features.
      -nFeatureImputed <gene_feature> (germline|mrca)
                             Export nucleotide sequence using letters from germline (marked
                               lowercase) for uncovered regions.
      -allNFeaturesImputed [<from_reference_point> <to_reference_point>] (germline|mrca)
                             Export nucleotide sequences for all covered gene features. By default,
                               boundaries will be `FR1Begin FR4End`.
      -aaFeatureImputed <gene_feature> (germline|mrca)
                             Export amino acid sequence using letters from germline (marked
                               lowercase) for uncovered regions.
      -allAAFeaturesImputed [<from_reference_point> <to_reference_point>] (germline|mrca)
                             Export amino acid sequences for all covered gene features. By default,
                               boundaries will be `FR1Begin FR4End`.
