Formats

Annotation I/O

	VCF & BCF	GFF	GFF2 & GTF*	GFF3	BED
Specific Header / Metainformation	x	no header	no header		No header
Header line	x				no
CHROM	x	seqname	Reference sequence		x
feature***					Name (optional)
source			x	x
method			x	type
POS	x	start & end	start & end	start & end	start & end
thickStart					x (optional)
thickEnd					x (optional)
itemRgb					x (optional)
blockCount					x (optional)
blockSizes					x (optional)
blockStarts					x (optional)
ID	x			seqid
ALT	x
QUAL	x	score	score	score	score (optional)
strand		x	x	x	x (optional)
frame		x	phase	phase
group			x
FILTER	x
INFO****	x	attribute		attributes**** *
FORMAT**** ** (optional)	x
SAMPLES (optional)	x

*The GTF is identical to GFF version 2.

***Gene, Variation, Similarity

****INFO: Arbitrary keys are permitted, although some sub-fields are reserved (albeit optional).

**** *attributes: ID, Name, Alias, Parent, Target, Gap, Derives_from, Note, Dbxref, Ontology_term

**** **FORMAT Tags: AD, ADF, ADR, DP, EC, FT, GL, GP , GQ, GT, HQ, MQ, PL, PQ, PS

Input / Output:

Formats:

VCF (Variant Call Format), BCF, GFF (General Feature Format), GFF2 (deprecated), GTF (General Transfer Format), GFF3, BED (Browser Extensible Data), GVF

HGVS vs BED vs GVF vs VCF Format example: https://www.ncbi.nlm.nih.gov/variation/tools/reporter/docs/examples#section-1.2.3

Format Overviews of Broad Institute of MIT and Harvard and UCSC (University of California, Santa Cruz)

Format specification:

• VCF & BCF: https://samtools.github.io/hts-specs/VCFv4.3.pdf https://en.wikipedia.org/wiki/Variant_Call_Format
• GFF: https://www.ensembl.org/info/website/upload/gff.html
• GFF2: http://gmod.org/wiki/GFF2
• GFF3: http://gmod.org/wiki/GFF3 https://en.wikipedia.org/wiki/General_feature_format

Desired format conversions

VCF to GFF: http://seqanswers.com/forums/showthread.php?t=9796&highlight=gff+vcf%3C/a