WES

HTAN Whole Exome Sequencing Data Model Schema

CoreFileAttributes

Universal attributes that apply to all file-based data in HTAN

Attribute	Type	Required	Description
FILENAME	string	Yes	Name of the file
FILE_FORMAT	string	Yes	Format of the file (e.g., fastq, bam, vcf, h5ad)
HTAN_DATA_FILE_ID	string	Yes	HTAN Data File ID (Primary Key)
HTAN_PARENT_ID	string	Yes	HTAN Parent ID(s) - Foreign key(s) to parent entity (B for Biospecimen, D for data file). One or more IDs; for aggregated files provide multiple. Each ID must have B or D suffix. Supports HTA200-229 for phase 2.

BaseSequencingAttributes

Minimal base attributes shared across all sequencing types

Attribute	Type	Required	Description
CHECKSUM	string	No	Checksum for data integrity verification
FILENAME	string	Yes	Name of the file
FILE_FORMAT	string	Yes	Format of the file (e.g., fastq, bam, vcf, h5ad)
HTAN_DATA_FILE_ID	string	Yes	HTAN Data File ID (Primary Key)
HTAN_PARENT_ID	string	Yes	HTAN Parent ID(s) - Foreign key(s) to parent entity (B for Biospecimen, D for data file). One or more IDs; for aggregated files provide multiple. Each ID must have B or D suffix. Supports HTA200-229 for phase 2.

BaseSequencingLevel1Attributes

Level 1 attributes - sequencing run and library (raw data)

Attribute	Type	Required	Description
LIBRARY_LAYOUT	LibraryLayoutEnum	Yes	Library layout (paired-end or single-end)
SEQUENCING_PLATFORM	SequencingPlatformEnum	Yes	Sequencing platform used
SEQUENCING_BATCH_ID	string	No	Sequencing batch identifier
LIBRARY_PREPARATION_DAYS_FROM_INDEX	integer	No	Number of days between when the sample for assay was received in the lab and the libraries were prepared for sequencing. If not applicable please enter ‘Not Applicable’)
TECHNICAL_REPLICATE_GROUP	string	No	Technical replicate group identifier
PROTOCOL_LINK	string	No	Link to sequencing protocol
CHECKSUM	string	No	Checksum for data integrity verification
FILENAME	string	Yes	Name of the file
FILE_FORMAT	string	Yes	Format of the file (e.g., fastq, bam, vcf, h5ad)
HTAN_DATA_FILE_ID	string	Yes	HTAN Data File ID (Primary Key)
HTAN_PARENT_ID	string	Yes	HTAN Parent ID(s) - Foreign key(s) to parent entity (B for Biospecimen, D for data file). One or more IDs; for aggregated files provide multiple. Each ID must have B or D suffix. Supports HTA200-229 for phase 2.

BaseSequencingLevel2Attributes

Level 2 attributes - alignment and alignment workflow

Attribute	Type	Required	Description
GENOMIC_REFERENCE	GenomicReferenceEnum	Yes	Genomic or transcriptomic reference assembly used for alignment. If your genome reference is not among the valid values, please contact your data liaison.
GENOMIC_REFERENCE_URL	string	Yes	URL to genomic or transcriptomic reference
GENOME_ANNOTATION_URL	string	Yes	URL to genome or transcriptome annotation
WORKFLOW_VERSION	string	Yes	Major version of the workflow, or ‘Not applicable’ when no workflow version applies.
WORKFLOW_LINK	string	Yes	Link to workflow or command. DockStore.org recommended
LIBRARY_LAYOUT	LibraryLayoutEnum	Yes	Library layout (paired-end or single-end)
SEQUENCING_PLATFORM	SequencingPlatformEnum	Yes	Sequencing platform used
SEQUENCING_BATCH_ID	string	No	Sequencing batch identifier
LIBRARY_PREPARATION_DAYS_FROM_INDEX	integer	No	Number of days between when the sample for assay was received in the lab and the libraries were prepared for sequencing. If not applicable please enter ‘Not Applicable’)
TECHNICAL_REPLICATE_GROUP	string	No	Technical replicate group identifier
PROTOCOL_LINK	string	No	Link to sequencing protocol
CHECKSUM	string	No	Checksum for data integrity verification
FILENAME	string	Yes	Name of the file
FILE_FORMAT	string	Yes	Format of the file (e.g., fastq, bam, vcf, h5ad)
HTAN_DATA_FILE_ID	string	Yes	HTAN Data File ID (Primary Key)
HTAN_PARENT_ID	string	Yes	HTAN Parent ID(s) - Foreign key(s) to parent entity (B for Biospecimen, D for data file). One or more IDs; for aggregated files provide multiple. Each ID must have B or D suffix. Supports HTA200-229 for phase 2.

BaseSequencingLevel3Attributes

Level 3+ attributes - inherits alignment and workflow; used for processed/analysis levels

Attribute	Type	Required	Description
GENOMIC_REFERENCE	GenomicReferenceEnum	Yes	Genomic or transcriptomic reference assembly used for alignment. If your genome reference is not among the valid values, please contact your data liaison.
GENOMIC_REFERENCE_URL	string	Yes	URL to genomic or transcriptomic reference
GENOME_ANNOTATION_URL	string	Yes	URL to genome or transcriptome annotation
WORKFLOW_VERSION	string	Yes	Major version of the workflow, or ‘Not applicable’ when no workflow version applies.
WORKFLOW_LINK	string	Yes	Link to workflow or command. DockStore.org recommended
LIBRARY_LAYOUT	LibraryLayoutEnum	Yes	Library layout (paired-end or single-end)
SEQUENCING_PLATFORM	SequencingPlatformEnum	Yes	Sequencing platform used
SEQUENCING_BATCH_ID	string	No	Sequencing batch identifier
LIBRARY_PREPARATION_DAYS_FROM_INDEX	integer	No	Number of days between when the sample for assay was received in the lab and the libraries were prepared for sequencing. If not applicable please enter ‘Not Applicable’)
TECHNICAL_REPLICATE_GROUP	string	No	Technical replicate group identifier
PROTOCOL_LINK	string	No	Link to sequencing protocol
CHECKSUM	string	No	Checksum for data integrity verification
FILENAME	string	Yes	Name of the file
FILE_FORMAT	string	Yes	Format of the file (e.g., fastq, bam, vcf, h5ad)
HTAN_DATA_FILE_ID	string	Yes	HTAN Data File ID (Primary Key)
HTAN_PARENT_ID	string	Yes	HTAN Parent ID(s) - Foreign key(s) to parent entity (B for Biospecimen, D for data file). One or more IDs; for aggregated files provide multiple. Each ID must have B or D suffix. Supports HTA200-229 for phase 2.

BulkWESLevel1

Bulk Whole Exome Sequencing Level 1 - Raw files

Attribute	Type	Required	Description
FILE_FORMAT	string	Yes	Format of the raw sequencing file (fastq or fastq.gz)
FILENAME	string	Yes	Name of the file. Must end with an extension matching the FILE_FORMAT (.fastq for fastq; .fastq.gz or .fq.gz for fastq.gz)
READ_INDICATOR	string	No	Read indicator
LIBRARY_SELECTION_METHOD	LibrarySelectionMethodEnum	Yes	Method used for library selection
READ_LENGTH	integer	Yes	Read length in base pairs
TARGET_CAPTURE_KIT	string	No	Target capture kit used
LIBRARY_PREPARATION_KIT_NAME	string	No	Name of the library preparation kit
LIBRARY_PREPARATION_KIT_VENDOR	string	No	Vendor of the library preparation kit
LIBRARY_PREPARATION_KIT_VERSION	string	No	Version of the library preparation kit
ADAPTER_NAME	string	No	Name of the adapter used
ADAPTER_SEQUENCE	string	No	Adapter sequence
BASE_CALLER_NAME	string	No	Name of the base caller
BASE_CALLER_VERSION	string	No	Version of the base caller
FLOW_CELL_BARCODE	string	No	Flow cell barcode
FRAGMENT_MAXIMUM_LENGTH	integer	No	Maximum fragment length
FRAGMENT_MEAN_LENGTH	integer	No	Mean fragment length
FRAGMENT_MINIMUM_LENGTH	integer	No	Minimum fragment length
FRAGMENT_STANDARD_DEVIATION_LENGTH	integer	No	Standard deviation of fragment length
LANE_NUMBER	integer	No	Lane number
MULTIPLEX_BARCODE	string	No	Multiplex barcode
LIBRARY_PREPARATION_DAYS_FROM_INDEX	integer	No	Days from index for library preparation
SIZE_SELECTION_RANGE	string	No	Size selection range
TARGET_DEPTH	integer	No	Target sequencing depth
TO_TRIM_ADAPTER_SEQUENCE	boolean	No	Whether to trim adapter sequence
LIBRARY_LAYOUT	LibraryLayoutEnum	Yes	Library layout (paired-end or single-end)
SEQUENCING_PLATFORM	SequencingPlatformEnum	Yes	Sequencing platform used
SEQUENCING_BATCH_ID	string	No	Sequencing batch identifier
TECHNICAL_REPLICATE_GROUP	string	No	Technical replicate group identifier
PROTOCOL_LINK	string	No	Link to sequencing protocol
CHECKSUM	string	No	Checksum for data integrity verification
HTAN_DATA_FILE_ID	string	Yes	HTAN Data File ID (Primary Key)
HTAN_PARENT_ID	string	Yes	HTAN Parent ID(s) - Foreign key(s) to parent entity (B for Biospecimen, D for data file). One or more IDs; for aggregated files provide multiple. Each ID must have B or D suffix. Supports HTA200-229 for phase 2.

BulkWESLevel2

Bulk Whole Exome Sequencing Level 2 - Reads mapped to the genome and alignment QC

Attribute	Type	Required	Description
FILE_FORMAT	string	Yes	Format of the aligned file (bam or cram)
FILENAME	string	Yes	Name of the file. Must end with an extension matching the FILE_FORMAT (.bam for bam; .cram for cram)
ALIGNMENT_WORKFLOW_TYPE	string	Yes	Type of alignment workflow used
INDEX_FILE_NAME	string	No	Name of the index file
AVERAGE_BASE_QUALITY	float	No	Average base quality
AVERAGE_INSERT_SIZE	integer	No	Average insert size
AVERAGE_READ_LENGTH	integer	No	Average read length
CONTAMINATION	float	No	Contamination estimate
CONTAMINATION_ERROR	float	No	Contamination error estimate
MEAN_COVERAGE	float	Yes	Mean coverage depth
ADAPTER_CONTENT	string	No	Adapter content information
BASIC_STATISTICS	string	No	Basic statistics from QC
ENCODING	string	No	Encoding information
OVERREPRESENTED_SEQUENCES	string	No	Overrepresented sequences
PER_BASE_N_CONTENT	string	No	Per base N content
PER_BASE_SEQUENCE_CONTENT	string	No	Per base sequence content
PER_BASE_SEQUENCE_QUALITY	string	No	Per base sequence quality
PER_SEQUENCE_GC_CONTENT	string	No	Per sequence GC content
PER_SEQUENCE_QUALITY_SCORE	string	No	Per sequence quality score
PER_TILE_SEQUENCE_QUALITY	string	No	Per tile sequence quality
PERCENT_GC_CONTENT	float	No	Percent GC content
SEQUENCE_DUPLICATION_LEVELS	string	No	Sequence duplication levels
SEQUENCE_LENGTH_DISTRIBUTION	string	No	Sequence length distribution
QC_WORKFLOW_TYPE	string	No	QC workflow type
QC_WORKFLOW_VERSION	string	No	QC workflow version
QC_WORKFLOW_LINK	string	No	Link to QC workflow
PAIRS_ON_DIFF_CHR	integer	No	Number of read pairs on different chromosomes
TOTAL_READS	integer	Yes	Total number of reads
TOTAL_UNIQUELY_MAPPED	integer	Yes	Total number of uniquely mapped reads
TOTAL_UNMAPPED_READS	integer	Yes	Total number of unmapped reads
PROPORTION_READS_DUPLICATED	float	No	Proportion of duplicated reads
PROPORTION_READS_MAPPED	float	Yes	Proportion of mapped reads
PROPORTION_TARGETS_NO_COVERAGE	float	No	Proportion of targets with no coverage
PROPORTION_BASE_MISMATCH	float	No	Proportion of base mismatches
SHORT_READS	integer	No	Number of short reads
PROPORTION_COVERAGE_10X	float	No	Proportion of coverage at 10x
PROPORTION_COVERAGE_30X	float	No	Proportion of coverage at 30x
IS_LOWEST_LEVEL	boolean	No	Whether this is the lowest level
GENOMIC_REFERENCE	GenomicReferenceEnum	Yes	Genomic or transcriptomic reference assembly used for alignment. If your genome reference is not among the valid values, please contact your data liaison.
GENOMIC_REFERENCE_URL	string	Yes	URL to genomic or transcriptomic reference
GENOME_ANNOTATION_URL	string	Yes	URL to genome or transcriptome annotation
WORKFLOW_VERSION	string	Yes	Major version of the workflow, or ‘Not applicable’ when no workflow version applies.
WORKFLOW_LINK	string	Yes	Link to workflow or command. DockStore.org recommended
LIBRARY_LAYOUT	LibraryLayoutEnum	Yes	Library layout (paired-end or single-end)
SEQUENCING_PLATFORM	SequencingPlatformEnum	Yes	Sequencing platform used
SEQUENCING_BATCH_ID	string	No	Sequencing batch identifier
LIBRARY_PREPARATION_DAYS_FROM_INDEX	integer	No	Number of days between when the sample for assay was received in the lab and the libraries were prepared for sequencing. If not applicable please enter ‘Not Applicable’)
TECHNICAL_REPLICATE_GROUP	string	No	Technical replicate group identifier
PROTOCOL_LINK	string	No	Link to sequencing protocol
CHECKSUM	string	No	Checksum for data integrity verification
HTAN_DATA_FILE_ID	string	Yes	HTAN Data File ID (Primary Key)
HTAN_PARENT_ID	string	Yes	HTAN Parent ID(s) - Foreign key(s) to parent entity (B for Biospecimen, D for data file). One or more IDs; for aggregated files provide multiple. Each ID must have B or D suffix. Supports HTA200-229 for phase 2.

BulkWESLevel3

Bulk Whole Exome Sequencing Level 3 - Called variants and MSI analysis

Attribute	Type	Required	Description
FILE_FORMAT	string	Yes	Format of the variant file (vcf or vcf.gz)
FILENAME	string	Yes	Name of the file. Must end with an extension matching the FILE_FORMAT (.vcf for vcf; .vcf.gz for vcf.gz)
GERMLINE_VARIANTS_WORKFLOW_URL	string	No	URL to the germline variants workflow
GERMLINE_VARIANTS_WORKFLOW_TYPE	string	No	Type of germline variants workflow
SOMATIC_VARIANTS_WORKFLOW_URL	string	No	URL to the somatic variants workflow
SOMATIC_VARIANTS_WORKFLOW_TYPE	string	No	Type of somatic variants workflow
SOMATIC_VARIANTS_SAMPLE_TYPE	SomaticVariantsSampleTypeEnum	No	Type of sample for somatic variants
STRUCTURAL_VARIANT_WORKFLOW_URL	string	No	URL to the structural variant workflow
STRUCTURAL_VARIANT_WORKFLOW_TYPE	string	No	Type of structural variant workflow
MSI_WORKFLOW_LINK	string	No	Link to MSI workflow
MSI_SCORE	float	No	MSI score
MSI_STATUS	MSIStatusEnum	No	MSI status
GENOMIC_REFERENCE	GenomicReferenceEnum	Yes	Genomic or transcriptomic reference assembly used for alignment. If your genome reference is not among the valid values, please contact your data liaison.
GENOMIC_REFERENCE_URL	string	Yes	URL to genomic or transcriptomic reference
GENOME_ANNOTATION_URL	string	Yes	URL to genome or transcriptome annotation
WORKFLOW_VERSION	string	Yes	Major version of the workflow, or ‘Not applicable’ when no workflow version applies.
WORKFLOW_LINK	string	Yes	Link to workflow or command. DockStore.org recommended
LIBRARY_LAYOUT	LibraryLayoutEnum	Yes	Library layout (paired-end or single-end)
SEQUENCING_PLATFORM	SequencingPlatformEnum	Yes	Sequencing platform used
SEQUENCING_BATCH_ID	string	No	Sequencing batch identifier
LIBRARY_PREPARATION_DAYS_FROM_INDEX	integer	No	Number of days between when the sample for assay was received in the lab and the libraries were prepared for sequencing. If not applicable please enter ‘Not Applicable’)
TECHNICAL_REPLICATE_GROUP	string	No	Technical replicate group identifier
PROTOCOL_LINK	string	No	Link to sequencing protocol
CHECKSUM	string	No	Checksum for data integrity verification
HTAN_DATA_FILE_ID	string	Yes	HTAN Data File ID (Primary Key)
HTAN_PARENT_ID	string	Yes	HTAN Parent ID(s) - Foreign key(s) to parent entity (B for Biospecimen, D for data file). One or more IDs; for aggregated files provide multiple. Each ID must have B or D suffix. Supports HTA200-229 for phase 2.

Enums

GenomicReferenceEnum

Genomic or transcriptomic reference assembly used for alignment

Value	Description
GRCh37	Genome Reference Consortium human build 37
GRCh37.p13	GRCh37 patch release 13
GRCh38	Genome Reference Consortium human build 38
GRCh38.p13	GRCh38 patch release 13
GRCh38.p14	GRCh38 patch release 14
hg19	UCSC human genome reference hg19
hg38	UCSC human genome reference hg38

LibraryLayoutEnum

Value	Description
Paired-end	Paired-end sequencing
Single-end	Single-end sequencing

LibrarySelectionMethodEnum

Value	Description
Hybrid Selection	Hybrid selection method
PCR	PCR-based selection
RANDOM	Random selection
other	Other selection method

MSIStatusEnum

Value	Description
MSI-H	High microsatellite instability
MSI-L	Low microsatellite instability
MSS	Microsatellite stable
Unknown	Unknown MSI status

SequencingPlatformEnum

Value	Description
ABI_SOLID	ABI SOLID sequencing platform
BGISEQ	BGI sequencing platform
CAPILLARY	Capillary sequencing platform
COMPLETE_GENOMICS	Complete Genomics sequencing platform
HELICOS	Helicos sequencing platform
ILLUMINA	Illumina sequencing platform
ION_TORRENT	Ion Torrent sequencing platform
LS454	454 sequencing platform
OXFORD_NANOPORE	Oxford Nanopore sequencing platform
PACBIO_SMRT	PacBio SMRT sequencing platform

SomaticVariantsSampleTypeEnum

Value	Description
Metastatic	Metastatic tumor sample
Normal	Normal tissue sample
Other	Other sample type
Primary	Primary tumor sample
Recurrent	Recurrent tumor sample