Yeast analysis example #70
Merged
Conversation
This file contains 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
Chris7
reviewed
Oct 23, 2024
| enter these details in future commands. | ||
|
|
||
| ```console | ||
| bvh@mbp:~$ gen init |
There was a problem hiding this comment.
we should remove the prefixes from your cpu so all this code is copy/pasteable without additional work
There was a problem hiding this comment.
Will do in my next goaround (David had some other suggestions to expand this example case)
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
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Outdated suggestions cannot be applied.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.
The bcftools wrangling that was required to get the variant calls to end up in the right block groups makes me think that gen should support some of these reassigments. Contig names I can see as being out of scope, but for samples we should be able to either import a vcf into a sample regardless of the sample name in the vcf, or have an operation where a new block_group is created by taking the union of two block_groups.
This document should be expanded with more interpretation and downstream analysis of the GFA files, and use of gen branching and checkout when switching strategies from variant stacking to genome alignment.