Add missing samtools, bedtools, beagle formats

[matuskalas]

Request from an email: Would it be possible for CRAM, CRAI and beagle to be added to the file formats to the ontology tree?

[cristynkells]

The latest CRAM and CRAI (corresponding index) file format specification can be found at https://samtools.github.io/hts-specs/ - specifically http://samtools.github.io/hts-specs/CRAMv3.pdf

The latest Beagle file format specification can be found at https://faculty.washington.edu/browning/beagle/ - specifically https://faculty.washington.edu/browning/beagle/beagle_5.4_18Mar22.pdf

[matuskalas]

Thank you so much @cristynkells 🙏🏽 This answered most of my questions before they were asked.

Beagle consumes and produces compressed VCF files. Is the Bref compression/format one needing to be added to EDAM?

[cristynkells]

Good idea on Bref:

The latest Bref3 file format specification can be found at https://faculty.washington.edu/browning/beagle - specifically https://faculty.washington.edu/browning/beagle/bref3.24May18.pdf

[JenniferShelton]

Could I add the BEDPE format to the list of additional data formats? The format is described here https://bedtools.readthedocs.io/en/latest/content/general-usage.html#bedpe-format

[cristynkells]

Hi @matuskalas, we are still not seeing CRAI, Beagle, Bref, BEDPE under the file formats to the ontology tree. We see CRAM was added. Thank you!

[allisonheath]

If I could chime with that we'd also like these (also saw CRAM but not CRAI) and then add tabix (.tbi) files as well: http://samtools.github.io/hts-specs/tabix.pdf ?

[M-casado]

Hi there, I think CSI files (htslib’s successor to the BAI index format) are also missing from Samtools' repertoire. Its file specifications can be found here.

Cheers, and thank you for your effort, guys! EDAM's format hierarchy is making my life way easier. We may soon rely on your ontology for metadata validation, so my name may pop-up in some other issues 😄