Phenopackets can be used to hold phenotypic information that can inform the analysis of sequencing data in VCF format as well as other high-throughput sequencing (HTS) or other data types. The HtsFile message allows a Phenopacket to link HTS files with data.

Given that HtsFile elements are listed in various locations such as the Phenopacket, Biosample, Family etc. which can in turn be nested, individual HTS files MUST be contained within their appropriate scope. For example within a Phenopacket for germline samples of an individual or within the scope of the Phenopacket.Biosample in the case of genomic data derived from sequencing that biosample. Aggregate data types such as Cohort and Family MUST contain aggregate HTS file data i.e. merged/multi-sample VCF at the level of the Family/Cohort, but each member Phenopacket can contain its own locally-scope HTS files pertaining to that individual/biosample(s).


This message is used for information about a high-throughput file.

Field Type Status Description
uri string required A valid URI e.g. file://data/file1.vcf.gz or
description string optional Arbitrary description of the file
hts_format HtsFormat required Indicates the format of the HTS file
genome_assembly string required The genome assembly used (e.g. GRCh38)
individual_to_sample_identifiers a map of string key: value recommended The mapping between the or to the sample identifier in the HTS file


This message is used for a file in one of the HTS formats.

Field Description
UNKNOWN An HTS file of unknown type.
SAM A SAM format file
BAM A BAM format file
CRAM A CRAM format file
VCF A VCF format file
BCF A BCF format file
GVCF A GVCF format file
FASTQ A FASTQ format file


    "uri": "file://data/genomes/germline_wgs.vcf.gz",
    "description": "Matched normal germline sample",
    "htsFormat": "VCF",
    "genomeAssembly": "GRCh38",
    "individualToSampleIdentifiers": {
      "patient23456": "NA12345"


URI for the file e.g. file://data/genomes/file1.vcf.gz or


An arbitrary description of the file contents.

The File message MUST have at least one of path and uri and usually should just have one of the two (in exceptional cases the same file might be referenced on a local file system and on the network).


This indicates which format the file has.


The genome assembly the contents of this file was called against. We recommend using the Genome Reference Consortium nomenclature e.g. GRCh37, GRCh38.


A map of identifiers mapping an individual refered to in the Phenopacket to a sample in the file. The key values must correspond to the Individual::id for the individuals in the message or Biosample::id for biosamples, the values must map to the samples in the HTS file.