# Format matrix

| Format    | Modality | Encoding | Multiple resolutions | Compression support[^1] | Index support | Authority |
|-----------|----------|----------|----------------------|-------------------------|---------------|-----------|
| FASTQ     | Sequence | Text     | No                  | BGZF                   |               | |
| FASTA     | Sequence | Text     | No                  | BGZF                   | FAI, FAI + GZI[^2]  | |
| SAM       | Alignment| Text     | No                  | BGZF                   | TBI, CSI      | [3] |
| BAM       | Alignment| Binary   | No               | BGZF                   | BAI, CSI      | [3] |
| VCF       | Variant call | Text | No                  | BGZF                   | TBI, CSI      | [3] |
| BCF       | Variant call | Binary | No           | BGZF                   | CSI           | [3] |
| GTF       | Feature  | Text     | No                  | BGZF                   | TBI, CSI      | |
| GFF3      | Feature  | Text     | No                  | BGZF                   | TBI, CSI      | [5] |
| BED       | Feature  | Text     | No                  | BGZF                   | TBI, CSI      | [3], [4] |
| BigBed    | Feature  | Binary   | Yes             | deflate                | Internal index |  [4] |
| BigWig    | Feature  | Binary   | Yes         | deflate                | Internal index | [4] |

[^1]: BGZF is a backwards-compatible "blocked" variant of GZIP that allows for random access and indexing using one of the companion index files listed in the next column.
[^2]: FAI indexes uncompressed FASTA records. GZI is an additional file required to perform look ups in BGZF-compressed FASTA.
[^3]: GA4GH and the [htslib](https://www.htslib.org/) references and specifications.
[^4]: UCSC Genome Browser and the [Kent Source](https://github.com/ucscGenomeBrowser/kent-core).
[^5]: [sequenceontology.org](https://github.com/The-Sequence-Ontology/Specifications/blob/master/gff3.md)