---
name: "CreateGermlines.py"
section: "1"
platform: "linux"
package: "changeo"
version: "1.3.0-3"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/CreateGermlines.py"
---

# CreateGermlines.py(1)

Repertoire clonal assignment toolkit (Python 3)

## NAME

CreateGermlines.py - Repertoire clonal assignment toolkit (Python 3)

## DESCRIPTION

usage: CreateGermlines.py \[--version\] \[-h\] **-d** DB\_FILES \[DB\_FILES ...\]

- \[-o OUT\_FILES \[OUT\_FILES ...\]\] \[--outdir OUT\_DIR\]

  \[--outname OUT\_NAME\] \[--log LOG\_FILE\] \[--failed\] \[--format {airr,changeo}\] **-r** REFERENCES \[REFERENCES ...\] \[-g {full,dmask,vonly,regions} \[{full,dmask,vonly,regions} ...\]\] \[--cloned\] \[--sf SEQ\_FIELD\] \[--vf V\_FIELD\] \[--df D\_FIELD\] \[--jf J\_FIELD\] \[--cf CLONE\_FIELD\]

Reconstructs germline sequences from alignment data

### help:

- **--version**

  show program's version number and exit

- **-h**, **--help**

  show this help message and exit

### standard arguments:

- **-d** DB\_FILES \[DB\_FILES ...\]

  A list of tab delimited database files. (default: None)

- **-o** OUT\_FILES \[OUT\_FILES ...\]

  Explicit output file name. Note, this argument cannot be used with the **--failed**, **--outdir**, or **--outname** arguments. If unspecified, then the output filename will be based on the input filename(s). (default: None)

- **--outdir** OUT\_DIR

  Specify to changes the output directory to the location specified. The input file directory is used if this is not specified. (default: None)

- **--outname** OUT\_NAME

  Changes the prefix of the successfully processed output file to the string specified. May not be specified with multiple input files. (default: None)

- **--log** LOG\_FILE

  Specify to write verbose logging to a file. May not be specified with multiple input files. (default: None)

- **--failed**

  If specified create files containing records that fail processing. (default: False)

- **--format** {airr,changeo}

  Specify input and output format. (default: airr)

### germline construction arguments:

- **-r** REFERENCES \[REFERENCES ...\]

  List of folders and/or fasta files (with .fasta, .fna or .fa extension) with germline sequences. When using the default Change-O sequence and coordinate fields, these reference sequences must contain IMGT-numbering spacers (gaps) in the V segment. Alternative numbering schemes, or no numbering, may work for alternative sequence and coordinate definitions that define a valid alignment, but a warning will be issued. (default: None)

- **-g** {full,dmask,vonly,regions} \[{full,dmask,vonly,regions} ...\]

  Specify type(s) of germlines to include full germline, germline with D segment masked, or germline for V segment only. (default: \['dmask'\])

- **--cloned**

  Specify to create only one germline per clone. Note, if allele calls are ambiguous within a clonal group, this will place the germline call used for the entire clone within the germline\_v\_call, germline\_d\_call and germline\_j\_call fields. (default: False)

- **--sf** SEQ\_FIELD

  Field containing the aligned sequence. Defaults to sequence\_alignment (airr) or SEQUENCE\_IMGT (changeo). (default: None)

- **--vf** V\_FIELD

  Field containing the germline V segment call. Defaults to v\_call (airr) or V\_CALL (changeo). (default: None)

- **--df** D\_FIELD

  Field containing the germline D segment call. Defaults to d\_call (airr) or D\_CALL (changeo). (default: None)

- **--jf** J\_FIELD

  Field containing the germline J segment call. Defaults to j\_call (airr) or J\_CALL (changeo). (default: None)

- **--cf** CLONE\_FIELD

  Field containing clone identifiers. Ignored if **--cloned** is not also specified. Defaults to clone\_id (airr) or CLONE (changeo). (default: None)

### output files:

-

  germ-pass

-

  database with assigned germline sequences.

-

  germ-fail

-

  database with records failing germline assignment.

### required fields:

-

  sequence\_id, sequence\_alignment, v\_call, d\_call, j\_call, v\_sequence\_start, v\_sequence\_end, v\_germline\_start, v\_germline\_end, d\_sequence\_start, d\_sequence\_end, d\_germline\_start, d\_germline\_end, j\_sequence\_start, j\_sequence\_end, j\_germline\_start, j\_germline\_end, np1\_length, np2\_length

### optional fields:

-

  n1\_length, n2\_length, p3v\_length, p5d\_length, p3d\_length, p5j\_length, clone\_id

### output fields:

-

  germline\_v\_call, germline\_d\_call, germline\_j\_call, germline\_alignment, germline\_alignment\_d\_mask, germline\_alignment\_v\_region, germline\_regions,

## AUTHOR

 This manpage was written by Nilesh Patra for the Debian distribution and\
  can be used for any other usage of the program.