-
Notifications
You must be signed in to change notification settings - Fork 34
New issue
Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.
By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.
Already on GitHub? Sign in to your account
Use target bed files as regions instead of bait intervals for SNV calling in WES samples #636
base: dev
Are you sure you want to change the base?
Conversation
|
I tried running a test case and the bed file presented to deepvariant can't be bgzipped.
|
CHANGELOG.md
Outdated
@@ -12,6 +12,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 | |||
### `Changed` | |||
|
|||
- Suffix used to identify unique fastq pairs from "\_T" to "\_LNUMBER" [#638](https://github.com/nf-core/raredisease/pull/638) | |||
- Change the regions used by deepavariant for WES samples from bait interval files to target bed files [#636](https://github.com/nf-core/raredisease/pull/636) |
There was a problem hiding this comment.
Choose a reason for hiding this comment
The reason will be displayed to describe this comment to others. Learn more.
Shouldn't the changelog just list the changes from version 2.2.0 to the next? This is more a fix of PR #633
There was a problem hiding this comment.
Choose a reason for hiding this comment
The reason will be displayed to describe this comment to others. Learn more.
Ah true.. I will remove it.
PR checklist
nf-core lint
).nextflow run . -profile test,docker --outdir <OUTDIR>
).nextflow run . -profile test_one_sample,docker --outdir <OUTDIR>
).nextflow run . -profile debug,test,docker --outdir <OUTDIR>
).docs/usage.md
is updated.docs/output.md
is updated.CHANGELOG.md
is updated.README.md
is updated (including new tool citations and authors/contributors).