-
Notifications
You must be signed in to change notification settings - Fork 18
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
Refactor gatk germline (resolves #280) #335
Merged
Merged
Changes from all commits
Commits
Show all changes
29 commits
Select commit
Hold shift + click to select a range
e0960dc
Refactor gatk germline (resolves #280)
jpfeil 95809f9
Add oncotator and synapse support (resolves #401)
jpfeil 9797429
Upload intermediate VCF
jpfeil e235c71
Use job to pass resource requirements
jpfeil 067302a
Addressed PR comments
jpfeil 01387fd
Fixed typos and add preprocess test
jpfeil e1be438
Fix memory passsing bug in preprocessing
jpfeil f6de579
Added defaults to config and manifest
jpfeil a3f0f11
Fix bug when realigning sorted BAM
jpfeil 3074706
Run hard filter independently
jpfeil 3b5c7ec
Refactored joint genotyping and filtering
jpfeil 1dc9457
Removed synapse and unnecessary common lib functions
jpfeil 33409be
Removed functions in common lib
jpfeil dc1958d
Removed split joint vcf by name
jpfeil 946442e
Add VQSR CLI and joint batching
jpfeil d858860
Improved batching method
jpfeil 7344019
Add CombineGVCFs
jpfeil 6936371
Add VQSR and joint genotype test
jpfeil 14b8ba1
Modified logging statements
jpfeil 6db248a
Add pipeline with VQSR test
jpfeil bcc27b8
Check number of samples earlier in the pipeline
jpfeil 1496221
Remove default resource values
jpfeil 12daa94
Update PromisedRequirements
jpfeil 84048e0
Sync germline lib modules with toil-lib
jpfeil 3f0877d
Add parameters for SNP and INDEL 1000G data
jpfeil 4c319e6
Added config requirements for each function
jpfeil 6dd338e
Use common lib generate file function
jpfeil be3f011
SQUASH: Add more documentation to the bwakit configuration function
jpfeil a51c70a
SQUASH: Addressed PR comments
jpfeil File filter
Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
There are no files selected for viewing
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
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
Oops, something went wrong.
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.
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.
Just to confirm here, we removed this import because
toil_scripts.gatk_processing.gatk_preprocessing
moved intotoil_scripts.gatk_germline.germline
, right?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.
That's correct.