A file containing alignment data in bam format.
| Name | Type | Description | Notes |
|---|---|---|---|
| controlled_access | character | Boolean value, indicating the file being controlled access, if true. | [optional] |
| anvil_url | character | URL linking to the controlled access file that has been deposited at AnVIL workspace. | [optional] |
| transcriptome_annotation | character | The annotation and version of the reference resource. | [optional] [Enum: [GENCODE 32, GENCODE 40, GENCODE 41, GENCODE 42, GENCODE 43, GENCODE 44, GENCODE 45, GENCODE 47, GENCODE Cast - M32, GENCODE M30, GENCODE M31, GENCODE M32, GENCODE M33, GENCODE M34, GENCODE M36]] |
| assembly | character | Genome assembly applicable for the annotation data. | [optional] [Enum: [Cast - GRCm39, GRCh38, GRCm39, custom]] |
| release_timestamp | character | The date the object was released. | [optional] |
| reference_files | set[character] | Link to the reference files used to generate this file. | [optional] |
| filtered | character | Indicates whether the file has gone through some filtering step, for example, removal of PCR duplicates or filtering based on significance calling. | [optional] |
| documents | set[character] | Documents that provide additional information (not data file). | [optional] |
| lab | character | Lab associated with the submission. | [optional] |
| award | character | Grant associated with the submission. | [optional] |
| accession | character | A unique identifier to be used to reference the object prefixed with IGVF. | [optional] |
| alternate_accessions | set[character] | Accessions previously assigned to objects that have been merged with this object. | [optional] |
| collections | set[character] | Some samples are part of particular data collections. | [optional] [Enum: ] |
| status | character | The status of the metadata object. | [optional] [Enum: [in progress, preview, released, deleted, replaced, revoked, archived]] |
| revoke_detail | character | Explanation of why an object was transitioned to the revoked status. | [optional] [Pattern: ^(\S+(\s |
| schema_version | character | The version of the JSON schema that the server uses to validate the object. | [optional] [Pattern: ^\d+(\.\d+)*$] |
| uuid | character | The unique identifier associated with every object. | [optional] |
| notes | character | DACC internal notes. | [optional] [Pattern: ^(\S+(\s |
| aliases | set[character] | Lab specific identifiers to reference an object. | [optional] |
| creation_timestamp | character | The date the object was created. | [optional] |
| submitted_by | character | The user who submitted the object. | [optional] |
| submitter_comment | character | Additional information specified by the submitter to be displayed as a comment on the portal. | [optional] [Pattern: ^(\S+(\s |
| description | character | A plain text description of the object. | [optional] [Pattern: ^(\S+(\s |
| analysis_step_version | character | The analysis step version of the file. | [optional] |
| content_md5sum | character | The MD5sum of the uncompressed file. | [optional] [Pattern: [a-f\d]{32} |
| content_type | character | The type of content in the file. | [optional] |
| dbxrefs | set[character] | Identifiers from external resources that may have 1-to-1 or 1-to-many relationships with IGVF file objects. | [optional] |
| derived_from | set[character] | The files participating as inputs into software to produce this output file. | [optional] |
| derived_manually | character | A boolean indicating whether the file has been dervided manually without automated computational methods. | [optional] |
| file_format | character | The file format or extension of the file. | [optional] [Enum: [bam]] |
| file_format_specifications | set[character] | Documents that describe the file format and fields of this file. | [optional] |
| file_set | character | The file set that this file belongs to. | [optional] |
| file_size | integer | File size specified in bytes. | [optional] [Min: 0] |
| md5sum | character | The md5sum of the file being transferred. | [optional] [Pattern: [a-f\d]{32} |
| submitted_file_name | character | Original name of the file. | [optional] |
| upload_status | character | The upload/validation status of the file. | [optional] [Enum: [pending, file not found, invalidated, validated, validation exempted]] |
| validation_error_detail | character | Explanation of why the file failed the automated content checks. | [optional] |
| checkfiles_version | character | The Checkfiles GitHub version release the file was validated with. | [optional] |
| read_count | integer | Number of reads in a bam file. Including both mapped, unmapped, and multi-mapped read counts. | [optional] [Min: 0] |
| redacted | character | Indicates whether the alignments data have been sanitized (redacted) to prevent leakage of private and potentially identifying genomic information. | [optional] |
| @id | character | [optional] | |
| @type | array[character] | [optional] | |
| summary | character | A summary of the alignment file. | [optional] |
| integrated_in | set[character] | Construct library set(s) that this file was used for in insert design. | [optional] |
| input_file_for | set[character] | The files which are derived from this file. | [optional] |
| gene_list_for | set[character] | File Set(s) that this file is a gene list for. | [optional] |
| loci_list_for | set[character] | File Set(s) that this file is a loci list for. | [optional] |
| assay_titles | set[character] | Title(s) of assay from the file set this file belongs to. | [optional] |
| workflow | character | The workflow used to produce this file. | [optional] |
| href | character | The download path to obtain file. | [optional] |
| s3_uri | character | The S3 URI of public file object. | [optional] |
| upload_credentials | object | The upload credentials for S3 to submit the file content. | [optional] |
| content_summary | character | A summary of the data in the alignment file. | [optional] |