Comments (3)
for whoever inherits this project: here are the locations of chrX imputations for PLCO as I've been informed by email:
/DCEG/CGF/Bioinformatics/Production/Shilpa/Projects/PLCO_chrX_Imputation/Oncoarray/IMPUTATION_1000G
/DCEG/CGF/Bioinformatics/Production/Shilpa/Projects/PLCO_chrX_Imputation/Oncoarray/IMPUTATION_TOPMED
/DCEG/CGF/Bioinformatics/Production/Shilpa/Projects/PLCO_chrX_Imputation/OmniX/IMPUTATION_TOPMED
/DCEG/CGF/Bioinformatics/Production/Shilpa/Projects/PLCO_chrX_Imputation/Omni25M/IMPUTATION_1000G
/DCEG/CGF/Bioinformatics/Production/Shilpa/Projects/PLCO_chrX_Imputation/Omni25M/IMPUTATION_TOPMED
/DCEG/CGF/Bioinformatics/Production/Shilpa/Projects/PLCO_chrX_Imputation/Omni5/IMPUTATION_1000G
/DCEG/CGF/Bioinformatics/Production/Shilpa/Projects/PLCO_chrX_Imputation/Omni5/IMPUTATION_TOPMED
/DCEG/CGF/Bioinformatics/Production/Shilpa/Projects/PLCO_chrX_Imputation/GSA/IMPUTATION_1000G/batch1 (batch2,batch3,batch4,batch5)
/DCEG/CGF/Bioinformatics/Production/Shilpa/Projects/PLCO_chrX_Imputation/GSA/IMPUTATION_TOPMED/batch1 (batch2,batch3,batch4,batch5)
from plco-analysis.
assorted comments:
- the 1KG variants of these imputations were for other testing purposes and should probably just be ignored for this project
- the TOPMed chrX imputation was performed using the open MIS variant, which seems to be vs TOPMed v8, whereas the autosomes (in imputation freeze 2) are vs the private server/TOPMed v5b. so they are not synced, and eventually the autosomes need to catch up to X
- the TOPMed chrX imputation was performed using chip data prepared for the first imputation pass, which is now deprecated. the biggest issues with this are (1) the ancestries were not split out before imputation, so the chips weren't appropriately cleaned; and (2) the batch assignments for freeze 2 were shuffled for GSA/Europeans to make them fit into 4 batches instead of 5, and since this wasn't what happened with chrX you have one additional chrX/GSA/European batch than you do for the autosomes
The above eventually just need to get synchronized, by everything getting reimputed to the public server's TOPMed panel with the better input prep. However, at least for the moment, I think the batch count discrepancy isn't that much of an issue (I think). There may be some step that assumes all chromosomes are present; but in general, the pipeline merely processes whatever is present. So it shouldn't be too hard to force it to use these files as-is.
from plco-analysis.
need to have a .sample file linked with each chromosome, in case the samples are slightly different between chromosome X and the autosomes (which is the case in PLCO)
from plco-analysis.
Related Issues (18)
- patch to installable version HOT 2
- custom max number of principal components estimated/used HOT 4
- replace git-lfs hosting with something, anything, elsewhere HOT 2
- Makefile.config extension handling assumes python=3 HOT 2
- readthedocs documentation
- modernize/update the checks
- update README with milestones HOT 1
- handing ordinal target variable in the pipeline fails when the sample size of one of the comparisons is below the threshold
- add case-inclusion and case-exclusion options HOT 1
- add ldsc workflow that does not depend on the file names/paths in the workflow
- error in aggregating results files in globus.Makefile
- categorical trait module expansion HOT 5
- tracking inspection HOT 2
- cleanup of incomplete pipelines HOT 5
- fix config check HOT 4
- clean up Makefile.config HOT 2
- project agnostic nomenclature/inputs HOT 6
Recommend Projects
-
React
A declarative, efficient, and flexible JavaScript library for building user interfaces.
-
Vue.js
🖖 Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.
-
Typescript
TypeScript is a superset of JavaScript that compiles to clean JavaScript output.
-
TensorFlow
An Open Source Machine Learning Framework for Everyone
-
Django
The Web framework for perfectionists with deadlines.
-
Laravel
A PHP framework for web artisans
-
D3
Bring data to life with SVG, Canvas and HTML. 📊📈🎉
-
Recommend Topics
-
javascript
JavaScript (JS) is a lightweight interpreted programming language with first-class functions.
-
web
Some thing interesting about web. New door for the world.
-
server
A server is a program made to process requests and deliver data to clients.
-
Machine learning
Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.
-
Visualization
Some thing interesting about visualization, use data art
-
Game
Some thing interesting about game, make everyone happy.
Recommend Org
-
Facebook
We are working to build community through open source technology. NB: members must have two-factor auth.
-
Microsoft
Open source projects and samples from Microsoft.
-
Google
Google ❤️ Open Source for everyone.
-
Alibaba
Alibaba Open Source for everyone
-
D3
Data-Driven Documents codes.
-
Tencent
China tencent open source team.
from plco-analysis.