fix: add condition for prepending chr to variant chromosome#195
Merged
Conversation
add MiniGenome with non-standard contigs for testing fixes #194 also: add Macfas_6.0.115 annotation with removed chrMT due to it missing from MacFas6 assembly
SophiaPerzan-DG
approved these changes
Jan 30, 2026
s22chan
reviewed
Jan 30, 2026
|
|
||
| wget -O Macfas_6.0.115.gff3.gz ftp://ftp.ensembl.org/pub/release-115/gff3/macaca_fascicularis/Macaca_fascicularis.Macaca_fascicularis_6.0.115.gff3.gz | ||
|
|
||
| # MT appears in the gff3 but not in the macFas6 assembly files. |
Collaborator
There was a problem hiding this comment.
do you know if it's a merge? they did that with GRCh37
Collaborator
There was a problem hiding this comment.
logic_name=mt_genbank_import
looks like it
Contributor
Author
There was a problem hiding this comment.
What's the implication?
Collaborator
There was a problem hiding this comment.
nothing really, just that some gffs need a merged assembly (or for gk to be able to map one gff to multiple assemblies).
the only two situations I've seen this is:
MT - mitocondrial was sequenced separately
T2T - Y was a different sample, but that was pre-merged
DG may be ok without MT but not sure about the broader community
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
3 participants
Add this suggestion to a batch that can be applied as a single commit.This suggestion is invalid because no changes were made to the code.Suggestions cannot be applied while the pull request is closed.Suggestions cannot be applied while viewing a subset of changes.Only one suggestion per line can be applied in a batch.Add this suggestion to a batch that can be applied as a single commit.Applying suggestions on deleted lines is not supported.You must change the existing code in this line in order to create a valid suggestion.Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be applied on multi-line comments.Suggestions cannot be applied while the pull request is queued to merge.Suggestion cannot be applied right now. Please check back later.
add MiniGenome with non-standard contigs for testing
fixes #194
also: add Macfas_6.0.115 annotation
with removed chrMT due to it missing from MacFas6 assembly