Kirill Tsukanov
Kirill Tsukanov
Consider two files from this EFO release: https://github.com/EBISPOT/efo/releases/tag/v3.42.0. **`efo.owl`** is the whole ontology, while **`efo_otar_slim.owl`** is a subsection of it used for the purposes of the Open Targets project. Further...
# A suite of @d-cameron's PRs * [x] https://github.com/samtools/hts-specs/pull/465 Improved Structural Variant Support * [x] https://github.com/samtools/hts-specs/pull/468 Allow multiple SVs per record (housekeeping changes to ensure all SV fields allow for...
Originally reported by @jmarshall [here](https://github.com/samtools/hts-specs/pull/456#pullrequestreview-658934972) --- Two remaining minor issues that we might wish to address as followups (but that should not delay this PR today): * Rob's comment about...
Originally raised by @julesjacobsen as part of [discussions](https://github.com/samtools/hts-specs/pull/465/files#r370675441) in #465 --- Has there been any further discussion about this? I'd like to propose a slight shift in the way things...
These fields use a lot of common semantics and variation types, which should be unified specification-wide as much as possible. See also #469.
Raised as [part of discussions](https://github.com/samtools/hts-specs/pull/465/files#r371978302) in #465 @cwhelan > Is `` a valid first-level symbolic alt (which I think this language implies) according to this PR, or do breakend alts...
Comments extracted from discussions ([1](https://github.com/samtools/hts-specs/pull/465/files#r370681229), [2](https://github.com/samtools/hts-specs/pull/465/files#r370650146)) in #465 @cwhelan > I might add that there's also the option to use `` for a duplication if you know it exists but...
As discussed during GA4GH Connect 2021 calls: @d-cameron > Just checked VCFv4.3: MD5 isn't even formally defined as a ##contig header field. We should add both ga4gh & md5 into...
E.g. page 16 in https://samtools.github.io/hts-specs/VCFv4.3.pdf, as this significantly impairs readability. As one option, just extract all examples into a separate document to avoid cluttering the specification.
Created from @cwhelan comments on https://github.com/samtools/hts-specs/pull/465 --- I think that this section could use a little clarification or a preamble stating what the valid use cases for using symbolic alleles...