Type: object
Description: A file in one of the HTS formats (https://samtools.github.io/hts-specs)

Properties

description

• type: string

description of the file contents

description Value Example

"this is the description for the file"

genomeAssembly

• type: string

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

genomeAssembly Value Example

"GRCh37"

htsFormat

• type:

one of UNKNOWN, SAM, BAM, CRAM, VCF, BCF, GVCF

htsFormat Value Example

"SAM"

individualToSampleIdentifiers

• type: object

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

individualToSampleIdentifiers Value Example

{
   "individual1" : "add example",
   "individual2" : "add example"
}

uri

• type: string

URI for the file

uri Value Examples

"file://data/genomes/file1.vcf.gz"

"https://opensnp.org/data/60.23andme-exome-vcf.231?1341012444"

HtsFile Value Example

{
   "htsFormat" : "GVCF",
   "uri" : "file://data/genomes/file1.vcf.gz"
}