Data Standard¶
All Change-O tools supports both the classical Change-O standard and the new Adaptive Immune Receptor Repertoire (AIRR) standard.
The Change-O standard is a tab-delimited file format (.tab) with a set of predefine
column names. The standardized column names used by the Change-O format are shown in the table below.
Most tools do not require every column. The columns required by, and added by, each
individual tool are described in the commandline usage documentation.
If a columns contains multiple entries, such as ambiguous V
segment assignments, these nested extries are delimited by commas.
The ordering of the columns does not matter.
An API for input and output of the Change-O format is provide in
changeo.IO.ChangeoReader and changeo.IO.ChangeoWriter, respectively.
See changeo.Receptor.Receptor for a description of the data structure used by
the reader and writer classes.
| Column Name | Type | Description |
|---|---|---|
| MakeDb - Standard Annotations | ||
| SEQUENCE_ID | string | Unique sequence identifier |
| SEQUENCE_INPUT | string | Input nucleotide sequence |
| SEQUENCE_VDJ | string | V(D)J nucleotide sequence |
| SEQUENCE_IMGT | string | IMGT-numbered V(D)J nucleotide sequence |
| FUNCTIONAL | logical | T: V(D)J sequence is predicted to be productive |
| IN_FRAME | logical | T: junction region nucleotide sequence is in-frame |
| STOP | logical | T: stop codon is present in V(D)J nucleotide sequence |
| MUTATED_INVARIANT | logical | T: invariant amino acids properly encoded by V(D)J sequence |
| INDELS | logical | T: V(D)J nucleotide sequence contains insertions and/or deletions |
| LOCUS | string | Locus of the receptor |
| V_CALL | string | V allele assignment(s) |
| D_CALL | string | D allele assignment(s) |
| J_CALL | string | J allele assignment(s) |
| V_SEQ_START | integer | Position of first V nucleotide in SEQUENCE_INPUT |
| V_SEQ_LENGTH | integer | Number of V nucleotides in SEQUENCE_INPUT |
| V_GERM_START_IMGT | integer | Position of V_SEQ_START in IMGT-numbered germline V(D)J sequence |
| V_GERM_LENGTH_IMGT | integer | Length of the IMGT numbered germline V alignment |
| NP1_LENGTH | integer | Number of nucleotides between V and D segments |
| D_SEQ_START | integer | Position of first D nucleotide in SEQUENCE_INPUT |
| D_SEQ_LENGTH | integer | Number of D nucleotides in SEQUENCE_INPUT |
| D_GERM_START | integer | Position of D_SEQ_START in germline V(D)J nucleotide sequence |
| D_GERM_LENGTH | integer | Length of the germline D alignment |
| NP2_LENGTH | integer | Number of nucleotides between D and J segments |
| J_SEQ_START | integer | Position of first J nucleotide in SEQUENCE_INPUT |
| J_SEQ_LENGTH | integer | Number of J nucleotides in SEQUENCE_INPUT |
| J_GERM_START | integer | Position of J_SEQ_START in germline V(D)J nucleotide sequence |
| J_GERM_LENGTH | integer | Length of the germline J alignment |
| JUNCTION_LENGTH | integer | Number of junction nucleotides in SEQUENCE_VDJ |
| JUNCTION | string | Junction region nucletide sequence |
| MakeDb - Optional Region Annotations | ||
| FWR1_IMGT | string | IMGT-numbered FWR1 nucleotide sequence |
| FWR2_IMGT | string | IMGT-numbered FWR2 nucleotide sequence |
| FWR3_IMGT | string | IMGT-numbered FWR3 nucleotide sequence |
| FWR4_IMGT | string | IMGT-numbered FWR4 nucleotide sequence |
| CDR1_IMGT | string | IMGT-numbered CDR1 nucleotide sequence |
| CDR2_IMGT | string | IMGT-numbered CDR2 nucleotide sequence |
| CDR3_IMGT | string | IMGT-numbered CDR3 nucleotide sequence |
| MakeDb - IMGT Optional Annotations | ||
| N1_LENGTH | integer | Untemplated nucleotides 5’ of the D segment |
| N2_LENGTH | integer | Untemplated Nucleotides 3’ of the D segment |
| P3V_LENGTH | integer | Palindromic nucleotides 3’ of the V segment |
| P5D_LENGTH | integer | Palindromic nucleotides 5’ of the D segment |
| P3D_LENGTH | integer | Palindromic nucleotides 3’ of the D segment |
| P5J_LENGTH | integer | Palindromic nucleotides 5’ of the J segment |
| D_FRAME | integer | D segment reading frame |
| V_SCORE | float | Alignment score for the V |
| V_IDENTITY | float | Alignment identity for the V |
| D_SCORE | float | Alignment score for the D |
| D_IDENTITY | float | Alignment identity for the D |
| J_SCORE | float | Alignment score for the J |
| J_IDENTITY | float | Alignment identity for the J |
| MakeDb - IgBLAST Optional Annotations | ||
| V_SCORE | float | Alignment score for the V |
| V_IDENTITY | float | Alignment identity for the V |
| V_EVALUE | float | E-value for the alignment of the V |
| V_CIGAR | string | CIGAR string for the alignment of the V |
| D_SCORE | float | Alignment score for the D |
| D_IDENTITY | float | Alignment identity for the D |
| D_EVALUE | float | E-value for the alignment of the D |
| D_CIGAR | string | CIGAR string for the alignment of the D |
| J_SCORE | float | Alignment score for the J |
| J_IDENTITY | float | Alignment identity for the J |
| J_EVALUE | float | E-value for the alignment of the J |
| J_CIGAR | string | CIGAR string for the alignment of the J |
| MakeDb - iHHMune-Align Optional Annotations | ||
| VDJ_SCORE | float | Alignment score for the V(D)J |
| MakeDb - 10X Annotations | ||
| CELL | string | Cell barcode |
| C_CALL | string | Cell Ranger C-region assignment |
| CONSCOUNT | integer | Read count of contig |
| UMICOUNT | integer | UMI count for the sequence |
| V_CALL_10X | string | Cell Ranger V assignment |
| D_CALL_10X | string | Cell Ranger D assignment |
| J_CALL_10X | string | Cell Ranger J assignment |
| JUNCTION_10X | string | Cell Ranger junction nucleotide sequence |
| JUNCTION_10X_AA | string | Cell Ranger junction amino acid sequence |
| CreateGermlines Annotations | ||
| GERMLINE_VDJ | string | Full unaligned germline V(D)J nucleotide sequence |
| GERMLINE_VDJ_V_REGION | string | Unaligned germline V segment nucleotide sequence |
| GERMLINE_VDJ_D_MASK | string | Unaligned germline V(D)J nucleotides sequence with Ns masking the NP1-D-NP2 regions |
| GERMLINE_IMGT | string | Full IMGT-numbered germline V(D)J nucleotide sequence |
| GERMLINE_IMGT_V_REGION | string | IMGT-numbered germline V segment nucleotide sequence |
| GERMLINE_IMGT_D_MASK | string | IMGT-numbered germline V(D)J nucleotide sequence with Ns masking the NP1-D-NP2 regions |
| GERMLINE_V_CALL | string | Clonal consensus germline V assignment |
| GERMLINE_D_CALL | string | Clonal consensus germline D assignment |
| GERMLINE_J_CALL | string | Clonal consensus germline J assignment |
| GERMLINE_REGIONS | string | String showing germline segments positions encoded as V, D, J, N, and P characters |
| DefineClones Annotations | ||
| CLONE | integer | Clonal grouping identifier |
| TIgGER Annotations | ||
| V_CALL_GENOTYPED | string | Adjusted V allele assignment(s) following TIgGER genotype inference |
| pRESTO Annotations | ||
| PRCONS | string | UMI consensus primer |
| PRIMER | string | list of primers |
| CONSCOUNT | integer | number of reads contributing to the UMI consensus sequence |
| DUPCOUNT | integer | copy number of the sequence |