-
Notifications
You must be signed in to change notification settings - Fork 16
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
feat: update cnvkit pons #1465
base: deduplicate_with_umi
Are you sure you want to change the base?
feat: update cnvkit pons #1465
Conversation
Codecov ReportAll modified and coverable lines are covered by tests ✅
Additional details and impacted files@@ Coverage Diff @@
## deduplicate_with_umi #1465 +/- ##
=====================================================
Coverage 99.48% 99.48%
=====================================================
Files 40 40
Lines 1957 1960 +3
=====================================================
+ Hits 1947 1950 +3
Misses 10 10
Flags with carried forward coverage won't be shown. Click here to find out more. ☔ View full report in Codecov by Sentry. |
## Added - padding of bed-regions for CNVkit to minimum 100 base
…SAMIC into update_cnvkit_pons
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.
Looks great, neat implementation 🧙♂️ 🪄
BALSAMIC/snakemake_rules/variant_calling/somatic_cnv_tumor_normal_tga.rule
Show resolved
Hide resolved
…ALSAMIC into deduplicate_with_umi
…ALSAMIC into deduplicate_with_umi
…ALSAMIC into deduplicate_with_umi
…ALSAMIC into deduplicate_with_umi
…ALSAMIC into deduplicate_with_umi
…ALSAMIC into deduplicate_with_umi
…ALSAMIC into deduplicate_with_umi
…ALSAMIC into deduplicate_with_umi
…ALSAMIC into deduplicate_with_umi
|
Description
THIS PR IS WAS BLOCKED BY THIS: https://github.com/Clinical-Genomics/target_capture_bed/issues/133
Now solved by this: #1469
With the change to the BAM files in the TGA workflows to start using UMIs for removing duplicates we will need to rebuild the PONs for all TGA workflows:
At the same time there are issues with the current GMSmyeloid PON with reports of noisy results which may be due to the fact that the PON was built using tumor samples and with a mix of samples from an earlier version of the panel. So while re-building the PON we might take the time to choose better samples if any are available.
Also for the other panels it would be good to re-evaluate which samples we have and can use to make sure that we're using samples that are up to date with our methods.
Finally, we can see if there are any other panels available for which we have enough samples to create a PON. Such as the one mentioned here: #1460
Tasks:
Added google-sheet here: https://docs.google.com/spreadsheets/d/18vs_2MKk-IyByjGMqEptdSlfcn9mB9bbpx6DahCA_a4/edit?gid=1393363517#gid=1393363517
Added
Changed
Documentation
Tests
Feature Tests
Pipeline Integrity Tests
.hk
file)Clinical Genomics Stockholm
Documentation
Panel of Normal specific criteria
User Changes
Infrastructure Changes
Checklist
Important
Ensure that all checkboxes below are ticked before merging.
For Developers
For Reviewers
conditions where applicable, with satisfactory results.