$ simple_study_import.py --help
usage: simple_study_import.py [-h] [--verbose] [--ped-family PED_FAMILY]
[--ped-person PED_PERSON] [--ped-mom PED_MOM]
[--ped-dad PED_DAD] [--ped-sex PED_SEX]
[--ped-status PED_STATUS] [--ped-role PED_ROLE]
[--ped-no-role] [--ped-proband PED_PROBAND]
[--ped-no-header]
[--ped-file-format PED_FILE_FORMAT]
[--ped-layout-mode PED_LAYOUT_MODE]
[--ped-sep PED_SEP] [--id <study ID>]
[--vcf-files <VCF filename> [<VCF filename> ...]]
[--denovo-file <de Novo variants filename>]
[--cnv-file <CNV variants filename>]
[--dae-summary-file <summary filename>]
[-o <output directory>] [--skip-reports]
[--genotype-storage <genotype storage id>]
[--study-config STUDY_CONFIG] [--force]
[--denovo-variant DENOVO_VARIANT]
[--denovo-ref DENOVO_REF]
[--denovo-alt DENOVO_ALT]
[--denovo-location DENOVO_LOCATION]
[--denovo-chrom DENOVO_CHROM]
[--denovo-pos DENOVO_POS]
[--denovo-family-id DENOVO_FAMILY_ID]
[--denovo-best-state DENOVO_BEST_STATE]
[--denovo-genotype DENOVO_GENOTYPE]
[--denovo-person-id DENOVO_PERSON_ID]
[--denovo-sep DENOVO_SEP]
[--vcf-include-reference-genotypes]
[--vcf-include-unknown-family-genotypes]
[--vcf-include-unknown-person-genotypes]
[--vcf-multi-loader-fill-in-mode VCF_MULTI_LOADER_FILL_IN_MODE]
[--vcf-denovo-mode VCF_DENOVO_MODE]
[--vcf-omission-mode VCF_OMISSION_MODE]
[--vcf-pedigree-mode VCF_PEDIGREE_MODE]
[--vcf-chromosomes VCF_CHROMOSOMES]
[--dae-include-reference-genotypes]
[--add-chrom-prefix ADD_CHROM_PREFIX]
[--del-chrom-prefix DEL_CHROM_PREFIX]
[--cnv-location CNV_LOCATION]
[--cnv-chrom CNV_CHROM] [--cnv-start CNV_START]
[--cnv-end CNV_END]
[--cnv-family-id CNV_FAMILY_ID]
[--cnv-best-state CNV_BEST_STATE]
[--cnv-person-id CNV_PERSON_ID]
[--cnv-variant-type CNV_VARIANT_TYPE]
[--cnv-plus-values CNV_PLUS_VALUES]
[--cnv-minus-values CNV_MINUS_VALUES]
[--cnv-sep CNV_SEP]
[--cnv-transmission-type CNV_TRANSMISSION_TYPE]
<families filename>
simple import of new study data
positional arguments:
<families filename> families filename in pedigree or simple family format
optional arguments:
-h, --help show this help message and exit
--verbose, -V
--ped-family PED_FAMILY
specify the name of the column in the pedigree file
that holds the ID of the family the person belongs to
[default: familyId]
--ped-person PED_PERSON
specify the name of the column in the pedigree file
that holds the person's ID [default: personId]
--ped-mom PED_MOM specify the name of the column in the pedigree file
that holds the ID of the person's mother [default:
momId]
--ped-dad PED_DAD specify the name of the column in the pedigree file
that holds the ID of the person's father [default:
dadId]
--ped-sex PED_SEX specify the name of the column in the pedigree file
that holds the sex of the person [default: sex]
--ped-status PED_STATUS
specify the name of the column in the pedigree file
that holds the status of the person [default: status]
--ped-role PED_ROLE specify the name of the column in the pedigree file
that holds the role of the person [default: role]
--ped-no-role indicates that the provided pedigree file has no role
column. If this argument is provided, the import tool
will guess the roles of individuals and write them in
a "role" column.
--ped-proband PED_PROBAND
specify the name of the column in the pedigree file
that specifies persons with role `proband`; this
columns is used only when option `--ped-no-role` is
specified. [default: None]
--ped-no-header indicates that the provided pedigree file has no
header. The pedigree column arguments will accept
indices if this argument is given. [default: False]
--ped-file-format PED_FILE_FORMAT
Families file format. It should `pedigree` or
`simple`for simple family format [default: pedigree]
--ped-layout-mode PED_LAYOUT_MODE
Layout mode specifies how pedigrees drawing of each
family is handled. Available options are `generate`
and `load`. When layout mode option is set to generate
the loadertryes to generate a layout for the family
pedigree. When `load` is specified, the loader tries
to load the layout from the layout column of the
pedigree. [default: load]
--ped-sep PED_SEP Families file field separator [default: `\t`]
--id <study ID>, --study-id <study ID>
Unique study ID to use. If not specified the basename
of the family pedigree file is used for study ID
--vcf-files <VCF filename> [<VCF filename> ...]
VCF file to import
--denovo-file <de Novo variants filename>
DAE denovo variants file
--cnv-file <CNV variants filename>
CNV variants file
--dae-summary-file <summary filename>
DAE transmitted summary variants file to import
-o <output directory>, --out <output directory>
output directory for storing intermediate parquet
files. If none specified, "parquet/" directory inside
GPF instance study directory is used [default: None]
--skip-reports skip running report generation [default: False]
--genotype-storage <genotype storage id>, --gs <genotype storage id>
Id of defined in DAE.conf genotype storage [default:
genotype_filesystem]
--study-config STUDY_CONFIG
Config used to overwrite values in generated
configuration
--force, -F allows overwriting configuration file in case target
directory already contains such file
--denovo-variant DENOVO_VARIANT
The label or index of the column containing the CSHL-
style representation of the variant.[Default: variant]
--denovo-ref DENOVO_REF
The label or index of the column containing the
reference allele for the variant. [Default: none]
--denovo-alt DENOVO_ALT
The label or index of the column containing the
alternative allele for the variant. [Default: none]
--denovo-location DENOVO_LOCATION
The label or index of the column containing the CSHL-
style location of the variant. [Default: location]
--denovo-chrom DENOVO_CHROM
The label or index of the column containing the
chromosome upon which the variant is located.
[Default: none]
--denovo-pos DENOVO_POS
The label or index of the column containing the
position upon which the variant is located. [Default:
none]
--denovo-family-id DENOVO_FAMILY_ID
The label or index of the column containing the
family's ID. [Default: familyId]
--denovo-best-state DENOVO_BEST_STATE
The label or index of the column containing the best
state for the family. [Default: bestState]
--denovo-genotype DENOVO_GENOTYPE
The label or index of the column containing the family
genotype. [Default: genotype]
--denovo-person-id DENOVO_PERSON_ID
The label or index of the column containing the
person's ID. [Default: none]
--denovo-sep DENOVO_SEP
Denovo file field separator [default: `\t`]
--vcf-include-reference-genotypes
include reference only variants [default_value: False]
--vcf-include-unknown-family-genotypes
include family variants with fully unknown genotype
[default: False]
--vcf-include-unknown-person-genotypes
include family variants with partially unknown
genotype [default: False]
--vcf-multi-loader-fill-in-mode VCF_MULTI_LOADER_FILL_IN_MODE
used for multi VCF files loader to fill missing
genotypes; supported values are `reference` or
`unknown`[default: reference]
--vcf-denovo-mode VCF_DENOVO_MODE
used for handling family variants with denovo
inheritance; supported values are: `denovo`,
`possible_denovo`, `ignore`; [default: ignore]
--vcf-omission-mode VCF_OMISSION_MODE
used for handling family variants with omission
inheritance; supported values are: `omission`,
`possible_omission`, `ignore`; [default: ignore]
--vcf-pedigree-mode VCF_PEDIGREE_MODE
used for handling missmathes between samples in VCFand
sample in pedigree file;supported values are:
'intersection', 'union', 'fixed';'fixed' mode means
that pedigree should be accept 'as is' without any
modifications; samples found in pedigree but not in
the VCF should be patched with unknown
genotype;[default: 'fixed']
--vcf-chromosomes VCF_CHROMOSOMES
specifies a list of filename template substitutions;
then specified variant filename(s) are treated as
templates and each occurent of `[vc]` is replaced
consecutively by elements of VCF wildcards list; by
default the list is empty and no substitution takes
place. [default: None]
--dae-include-reference-genotypes
fill in reference only variants [default: False]
--add-chrom-prefix ADD_CHROM_PREFIX
Add specified prefix to each chromosome name in
variants file
--del-chrom-prefix DEL_CHROM_PREFIX
Remove specified prefix to each chromosome name in
variants file
--cnv-location CNV_LOCATION
The label or index of the column containing the CSHL-
style location of the variant. [Default: location]
--cnv-chrom CNV_CHROM
The label or index of the column containing the
chromosome of the variant. [Default: chrom]
--cnv-start CNV_START
The label or index of the column containing the start
of the CNV. [Default: pos]
--cnv-end CNV_END The label or index of the column containing the end of
the CNV variant. [Default: pos_end]
--cnv-family-id CNV_FAMILY_ID
The label or index of the column containing family's
ID. [Default: familyId]
--cnv-best-state CNV_BEST_STATE
The label or index of the column containing the
variant's best state. [Default: bestState]
--cnv-person-id CNV_PERSON_ID
The label or index of the column containing the ids of
the people in which the variant is. [Default: None]
--cnv-variant-type CNV_VARIANT_TYPE
The label or index of the column containing the
variant's type. [Default: variant]
--cnv-plus-values CNV_PLUS_VALUES
The cnv+ value used in the columns containing the
variant's type. [Default: CNV+]
--cnv-minus-values CNV_MINUS_VALUES
The cnv- value used in the columns containing the
variant's type. [Default: CNV-]
--cnv-sep CNV_SEP CNV file field separator. [Default: `\t`]
--cnv-transmission-type CNV_TRANSMISSION_TYPE
CNV transmission type. [Default: `denovo`]