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10x Genomics
Chromium Single Cell Immune Profiling

Cell Ranger3.0, printed on 11/23/2024

V(D)J Annotations

cellranger vdj pipeline produces V(D)J annotations on the assembled contigs and on the clonotype consensus sequences in multiple formats.

File type overview

File type Description
CSV High-level annotations with one contig, consensus, or clonotype per row.
JSON Detailed annotations, including alignment coordinates and amino acid translations.
BED Germline V(D)J segments as features, for use with a tool like IGV.

Annotation files

File Description
clonotypes.csv High-level descriptions of each clonotype.
consensus_annotations.{csv,json} High-level and detailed annotations of each clonotype consensus sequence.
filtered_contig_annotations.csv High-level annotations of each high-confidence, cellular contig. This is a subset of all_contig_annotations.csv.
all_contig_annotations.{csv,bed,json} High-level and detailed annotations of each contig.

Clonotype CSV file (clonotypes.csv)

Column Description
clonotype_id The ID of the clonotype to which this consensus sequence was assigned.
frequency The observed number of cell-barcodes with this clonotype.
proportion The observed fraction of cell-barcodes with this clonotype.
cdr3s_aa A semicolon-delimited list of chain:sequence pairs, where "chain" is e.g., TRA, TRB, IGK, IGL, or IGH and "sequence" is the CDR3 amino acid sequence for that chain.
cdr3s_nt A semicolon-delimited list of chain:sequence pairs, where "chain" is e.g., TRA, TRB, IGK, IGL, or IGH and "sequence" is the CDR3 nucleotide sequence for that chain.

Contig annotation CSV files (*contig_annotations.csv)

Name Description
barcode Cell-barcode for this contig.
is_cell True or False value indicating whether the barcode was called as a cell.
contig_id Unique identifier for this contig.
high_confidence True or False value indicating whether the contig was called as high-confidence (unlikely to be a chimeric sequence or some other artifact).
length The contig sequence length in nucleotides.
chain The chain associated with this contig; e.g., "TRA", "TRB", "IGK", "IGL", or "IGH". A value of "Multi" indicates that segments from multiple chains were present.
v_gene The highest-scoring V segment, e.g., TRAV1-1.
d_gene The highest-scoring D segment, e.g., TRBD1.
j_gene The highest-scoring J segment, e.g., TRAJ1-1.
c_gene The highest-scoring C segment, e.g., TRAC.
full_length A contig annotation is termed full-length if it has a valid V annotation (the contig aligns with at least 50% of the length of any V gene in the reference) and has a J gene annotation that spans until the 3′ end of the J region within one codon.
productive True, False, or None value predicting whether the transcript translates to a protein with a CDR3 region. "None" indicates that a prediction could not be made.
cdr3 The predicted CDR3 amino acid sequence.
cdr3_nt The predicted CDR3 nucleotide sequence.
reads The number of reads aligned to this contig.
umis The number of distinct UMIs aligned to this contig.
raw_clonotype_id The ID of the clonotype to which this cell-barcode was assigned.
raw_consensus_id The ID of the consensus sequence to which this contig was assigned.

Consensus annotation CSV files (consensus_annotations.csv)

Column Description
clonotype_id The ID of the clonotype to which this consensus sequence was assigned.
consensus_id The ID of this consensus sequence.

The remaining columns are shared with those under the "Contig annotation CSV files" section.