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Ingest CanDIG data

POST
/genomic

Ingest genomic data into CanDIG (maintained for backwards compatibility)

Parameters

Query Parameters

do_not_index
boolean

Set to true to prevent indexing of genomic files

Request Body

One of:
object
experiments
required
Array<object>

Describes the sequencing experiment performed on a specific specimen from a donor

object
program_id
required

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

string
experiment_id
required

Unique identifier given by the sequencing centre

string
submitter_sample_id
required

Unique identifier for the sample submitted for sequencing. Equivalent to MoHCCN’s submitter_sample_id in the Sample Registration schema.

string
metadata
required

Additional data that describes the sequencing experiment

object
library_description

Free text description of the library

string
instrument

Sequencing instrument used

string
Allowed values: ABI SOLID Models AB 5500 Genetic Analyzer AB 5500xl Genetic Analyzer AB 5500xl-W Genetic Analysis System AB SOLiD 3 Plus System AB SOLiD 4 System AB SOLiD 4hq System AB SOLiD PI System AB SOLiD System AB SOLiD System 2.0 AB SOLiD System 3.0 AB 310 Genetic Analyzer CAPILLARY Models AB 3130 Genetic Analyzer AB 3130xL Genetic Analyzer AB 3500 Genetic Analyzer AB 3500xL Genetic Analyzer AB 3730 Genetic Analyzer AB 3730xL Genetic Analyzer COMPLETE GENOMICS Models Complete Genomics HELICOS Models Helicos HeliScope ILLUMINA Models HiSeq X Five HiSeq X Ten Illumina Genome Analyzer Illumina Genome Analyzer II Illumina Genome Analyzer IIx Illumina HiScanSQ Illumina HiSeq 1000 Illumina HiSeq 1500 Illumina HiSeq 2000 Illumina HiSeq 2500 Illumina HiSeq 3000 Illumina HiSeq 4000 Illumina MiSeq Illumina MiniSeq Illumina NovaSeq 6000 NextSeq 500 NextSeq 550 ION TORRENT Models Ion Torrent PGM Ion Torrent Proton Ion Torrent S5 Ion Torrent S5 XL LS454 Models 454 GS 454 GS 20 454 GS FLX 454 GS FLX Titanium 454 GS FLX+ 454 GS Junior OXFORD NANOPORE Models GridION MinION PromethION PACBIO SMRT Models PacBio RS PacBio RS II Sequel
library_selection

Method used to enrich target

string
Allowed values: 5-methylcytidine antibody CAGE ChIP ChIP-Seq DNase HMPR Hybrid Selection Inverse rRNA Inverse rRNA selection MBD2 protein methyl-CpG binding domain MDA MF MNase MSLL Oligo-dT PCR PolyA RACE RANDOM RANDOM PCR RT-PCR Reduced Representation Restriction Digest cDNA cDNA_oligo_dT cDNA_randomPriming other padlock probes capture method repeat fractionation size fractionation unspecified
protocol

Optional link to protocol

string
library_source

Type of material

string
Allowed values: genomic genomic single cell metagenomic metatranscriptomic other synthetic transcriptomic transcriptomic single cell viral RNA
library_strategy
required

Type of data sequenced (whole genome or whole transcriptome)

string
Allowed values: AMPLICON ATAC-seq Bisulfite-Seq CLONE CLONEEND CTS ChIA-PET ChIP-Seq DNase-Hypersensitivity EST FAIRE-seq FINISHING FL-cDNA Hi-C MBD-Seq MNase-Seq MRE-Seq MeDIP-Seq OTHER POOLCLONE RAD-Seq RIP-Seq RNA-Seq SELEX Synthetic-Long-Read Targeted-Capture Tethered Chromatin Conformation Capture Tn-Seq VALIDATION WCS WGA WGS WXS miRNA-Seq ncRNA-Seq ssRNA-seq
library_layout

Single or Paired

string
Allowed values: paired single
analyses
required
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
analysis_id
required

A unique name for this downstream analysis

string
metadata
required

Additional data that describes the downstream analysis

object
analysis_type
required

Type of data represented in the Analysis

string
Allowed values: reference_alignment sequence_variation sequence_annotation
analysis_attribute
object
subtype

Specific subtype of analysis

string
expression_count
reference
required

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

string
default: hg38
Allowed values: hg37 hg38
reference_sequence_type
string
Allowed values: Whole genome sequencing Whole transcriptome sequencing Exome sequencing Genotyping by array transcriptomics Curation Genotyping by sequencing Target sequencing
reference_assembly_id

If provided, the name of the exact assembly used for the reference genome

string
analysis_centre

Name of sequencing centre that performed the analysis

string
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 Experiments and the samples in the analysis

Array<object>

Link between Experiments and the samples in the analysis

object
experiment_id
required

The ID of the sequencing experiment

string
analysis_sample_id
required

The name of the sample as listed in the analysis results

string
TUMOUR/NORMAL/PROGRAM_EXPERIMENT_ID_1

Responses

200

Success

object
queue_id

Queue ID to get status of ingest

string
warnings
Array<string>