CreateGermlines

Reconstructs germline sequences from alignment data

usage: CreateGermlines [--version] [-h] -d DB_FILES [DB_FILES ...]
                       [-o OUT_FILES [OUT_FILES ...]] [--outdir OUT_DIR]
                       [--outname OUT_NAME] [--log LOG_FILE] [--failed]
                       [--format {changeo,airr}] -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]

--version

show program’s version number and exit

-h, --help

show this help message and exit

-d <db_files>

A list of tab delimited database files.

-o <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).

--outdir <out_dir>

Specify to changes the output directory to the location specified. The input file directory is used if this is not specified.

--outname <out_name>

Changes the prefix of the successfully processed output file to the string specified. May not be specified with multiple input files.

--log <log_file>

Specify to write verbose logging to a file. May not be specified with multiple input files.

--failed

If specified create files containing records that fail processing.

--format {changeo,airr}

Specify input and output format.

-r <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.

-g {full,dmask,vonly,regions}

Specify type(s) of germlines to include full germline, germline with D segment masked, or germline for V segment only.

--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.

--sf <seq_field>

Field containing the aligned sequence. Defaults to SEQUENCE_IMGT (changeo) or sequence_alignment (airr).

--vf <v_field>

Field containing the germline V segment call. Defaults to V_CALL (changeo) or v_call (airr).

--df <d_field>

Field containing the germline D segment call. Defaults to D_CALL (changeo) or d_call (airr).

--jf <j_field>

Field containing the germline J segment call. Defaults to J_CALL (changeo) or j_call (airr).

output files:

germ-pass

database with assigned germline sequences.

germ-fail

database with records failing germline assignment.

required fields:

SEQUENCE_ID, SEQUENCE_IMGT, V_CALL, D_CALL, J_CALL, V_SEQ_START, V_SEQ_LENGTH, V_GERM_START_IMGT, V_GERM_LENGTH_IMGT, D_SEQ_START, D_SEQ_LENGTH, D_GERM_START, D_GERM_LENGTH, J_SEQ_START, J_SEQ_LENGTH, J_GERM_START, J_GERM_LENGTH, NP1_LENGTH, NP2_LENGTH

optional fields:

N1_LENGTH, N2_LENGTH, P3V_LENGTH, P5D_LENGTH, P3D_LENGTH, P5J_LENGTH, CLONE

output fields:

GERMLINE_IMGT, GERMLINE_IMGT_D_MASK, GERMLINE_IMGT_V_REGION, GERMLINE_V_CALL, GERMLINE_D_CALL, GERMLINE_J_CALL, GERMLINE_REGIONS