HtsFile sb-phenopackets

{S}[B] Status [i]
implemented
Provenance
Used by
Contributors
Source (v1.0.0)

Attributes

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

Properties

Property Type
description string
genomeAssembly string
htsFormat
individualToSampleIdentifiers object
uri string

description

description of the file contents

description Value Example
"this is the description for the file"

genomeAssembly

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

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

htsFormat Value Example
"SAM"

individualToSampleIdentifiers

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

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"
}