Table 2 The pragmas defined by GVF, in addition to those already defined by GFF3 (gff-version, sequence-region, feature-ontology, attribute-ontology, source-ontology, species, genome-build)
From: A standard variation file format for human genome sequences
Pragma | Allowed tags | Description |
|---|---|---|
file-version | Comment | This allows the specification of the version of a specific file. What exactly the version means is left undefined, but the tag is provided for the case when an individual's variants are described in GVF and then, at a later date, changes to the data or the software require an update to the file. An increment of the file-version could signify such a change. Any numeric version of file-version is allowed |
file-date | Comment | The file-date pragma is included as a method to describe the date when the file was created. The ISO 8601 standard for dates in the form YYYY-MM-DD is required for the value |
individual-id | Dbxref, Gender, Population, Comment | This pragma provides details about the individual whose variants are described in the file |
##individual-id Dbxref = Coriell:NA18507;Gender = male;Ethnicity = Yoruba; Comment = Yoruba from Ibadan | ||
source-method | Seqid, Source, Type, Dbxref, Comment | This pragma provides details about the algorithms or methodologies used to generate data for a given source in the file. This is used, for example, to document how a particular type of variant was called. A typical use would be to provide a DBxref link to a journal article describing software used for calling the variant data with the given source tag |
##source-method Seqid = chr1;Source = MAQ;Type = SNV;Dbxref = PMID:18714091;Comment = MAQ SNV calls; | ||
attribute-method | Seqid, Source, Type, Attribute, Dbxref, Comment | This pragma provides details about algorithms or methodologies for a given attribute tag in the file. This is used to document how a particular type of attribute value (that is, Genotype, Variant_effect) was calculated |
##attribute-method Source = SOLiD;Type = SNV;Attribute = Genotype;Comment = Genotype is reported here as determined in the original study | ||
technology-platform | Seqid, Source, Type, Read_length, Read_type, Read_pair_span, Platform_class, Platform_name, Average_coverage. Comment, Dbxref | This pragma provides details about the technologies (that is, sequencing or DNA microarray) used to generate the primary data |
##technology-platform Seqid = chr1;Source = AFFY_SNP_6;Type = SNV;Dbxref = URI:http://www.affymetrix.com; Platform_class = SNP_Array;Platform_name = Affymetrix Human SNP Array 6.0; | ||
data-source | Seqid, Source, Type, Dbxref, Data_type, Comment. | This pragma provides details about the source data for the variants contained in this file. This could be links to the actual sequence reads in a trace archive, or links to a variant file in another format that have been converted to GVF |
##data-source Source = MAQ;Type = SNV;Dbxref = SRA:SRA008175;Data_type = DNA sequence;Comment = NCBI Short Read Archive http://www.ncbi.nlm.nih.gov/Traces/sra; | ||
phenotype-description | Ontology, Term, Comment | A description of the phenotype of the individual. This pragma can contain either ontology constrained terms, or a free text description of the individual's phenotype or both. |
##phenotype-description Ontology = http://www.human-phenotype-ontology.org/human-phenotype-ontology.obo.gz;Term = acute myloid leukemia;Comment = AML relapse; | ||
ploidy | Ontology, Term, Comment | This pragma defines the ploidy for a given genome. This pragma can contain either ontology constrained terms, or a free text description of the individual's ploidy. It is suggested that ontology constrained terms use a subtype of the term PATO:0001374, which includes haploid, diploid, polyploid, triploid etc |
##ploidy chr22 1 49691432 diploid | ||
##ploidy chrY 1 57772954 haploid | ||