convert-variations
2.0
Performs inter-conversions between different formats of polymorphic variations.
Genome Variant Format (GVF), Variant Call Format (VCF) and RSAT variation format (varBed).
"The Genome Variant Format (GVF) is a type of GFF3 file with additional pragmas and attributes specified. The GVF format has the same nine column tab delimited format as GFF3 and all of the requirements and restrictions specified for GFF3 apply to the GVF specification as well." (quoted from the Sequence Ontology)
http://www.sequenceontology.org/resources/gvf_1.00.html
A GVF file starts with a header providing general information about the file content: format version, date, data source, length of the chromosomes / contigs covered by the variations.
##gff-version 3
##gvf-version 1.07
##file-date 2014-09-21
##genome-build ensembl GRCh38
##species http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=9606
##feature-ontology http://song.cvs.sourceforge.net/viewvc/song/ontology/so.obo?revision=1.283
##data-source Source=ensembl;version=77;url=http://e77.ensembl.org/Homo_sapiens
##file-version 77
##sequence-region Y 1 57227415
##sequence-region 17 1 83257441
##sequence-region 6 1 170805979
##sequence-region 1 1 248956422
## [...]This header is followed by the actual description of the variations, in a column-delimited format compying with the GFF format.
Y dbSNP SNV 10015 10015 . + . ID=1;variation_id=23299259;Variant_seq=C,G;Dbxref=dbSNP_138:rs113469508;allele_string=A,C,G;evidence_values=Multiple_observations;Reference_seq=A
Y dbSNP SNV 10146 10146 . + . ID=2;variation_id=26647928;Reference_seq=C;Variant_seq=G;evidence_values=Multiple_observations,1000Genomes;allele_string=C,G;Dbxref=dbSNP_138:rs138058540;global_minor_allele_frequency=0|0.0151515|33
Y dbSNP SNV 10153 10153 . + . ID=3;variation_id=21171339;Reference_seq=C;Variant_seq=G;evidence_values=Multiple_observations,1000Genomes;allele_string=C,G;Dbxref=dbSNP_138:rs111264342;global_minor_allele_frequency=1|0.00229568|5
Y dbSNP SNV 10181 10181 . + . ID=4;variation_id=47159994;Reference_seq=C;Variant_seq=G;evidence_values=1000Genomes;allele_string=C,G;Dbxref=dbSNP_138:rs189980076;global_minor_allele_frequency=0|0.00137741|3The last column contains a lot of relevant information, but is not very easy to read. We should keep in mind that this format was initially defined to describe generic genomic features, so all the specific attributes come in the last column (description).
http://en.wikipedia.org/wiki/Variant_Call_Format
This format was defined for the 1000 genomes project. It is no longer maintained. The converter supports it merely for the sake of backwards compatibility.
Tab-delimited format with a specific column order, used as input by retrieve-variation-seq.
This format presents several advantages for scanning variations with matrices.
A tab delimited file on selected output format.
Variation data that will be converted, supported formats: GVF, VCF or varBed.
Variation format of the input data, supported formats: GVF, VCF or varBed.
Variation format of the desired output data, supported formats: GVF, VCF or varBed