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Ingest Genomic data

POST
/genomic

Add linkages between clinical donors and genomic data.

Parameters

Query Parameters

do_not_index
boolean

Set to true to prevent indexing of genomic files

Request Body

Array<object>
object
program_id
required

Name of the program this sample belongs to. The user must be authorized to add data to this program.

string
genomic_file_id
required

A unique name for this genomic data resource

string
HG00096.vcf
metadata
required

Additional data that describes the genomic resource

object
sequence_type
required

Type of data sequenced (whole genome or whole transcriptome)

string
default: wgs
Allowed values: wgs wts
data_type
required

Type of data represented in the resource (variant or read)

string
Allowed values: variant read
reference
required

Which reference genome was used for alignment (hg37 or hg38)

string
default: hg38
Allowed values: hg37 hg38
main
required

Object describing a file

object
name
required

Name of the file, including all extensions

string
access_method
required
One of:

A description of an S3 URI. NB: even though the s3 prefix is incorrect, we allow it in parsing so that we can give better feedback to the user if a url is provided in that form.

string
/(https*|s3):\/\/(.+)\/(.+)\/(.+)/ 
http://s3.us-east-1.amazonaws.com/1000genomes/HG00096.vcf.gz
index
required

Object describing a file

object
name
required

Name of the file, including all extensions

string
access_method
required
One of:

A description of an S3 URI. NB: even though the s3 prefix is incorrect, we allow it in parsing so that we can give better feedback to the user if a url is provided in that form.

string
/(https*|s3):\/\/(.+)\/(.+)\/(.+)/ 
http://s3.us-east-1.amazonaws.com/1000genomes/HG00096.vcf.gz
samples
required

An array of links between donor data (e.g. MoH Sample Registrations) and the samples in the genomic data resource

Array<object>

Link between donor data (e.g. MoH Sample Registrations) and the samples in the genomic data resource

object
submitter_sample_id
required

The name of the sample as listed in the linked donor data

string
sample_registration_id_1
genomic_file_sample_id
required

The name of the sample in the genomic data resource

string
TUMOUR/NORMAL/PROGRAM_SAMPLE_REGISTRATION_ID_1

Responses

200

Success

object
queue_id

Queue ID to get status of ingest

string
warnings
Array<string>