Skip to content

Issues: NCI-CGR/GwasQcPipeline

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.

Sign up for GitHub

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

19 Open 200 Closed
19 Open 200 Closed
Author
Filter by author
Loading
Label
Filter by label
Loading
Use alt + click/return to exclude labels
or ⇧ + click/return for logical OR
Projects
Filter by project
Loading
Milestones
Filter by milestone
Loading
Assignee
Filter by who’s assigned
Sort
Sort by
Newest Oldest Most commented Least commented Recently updated Least recently updated Best match
Most reactions
👍 👎 😄 🎉 😕 ❤️ 🚀 👀

Issues list

Main Snakefile DAG should replicate the subworkflow DAG in an identical manner. workflow Anything related to snakemake componenets
#379 opened Feb 24, 2025 by rajwanir
1
@rajwanir
Missing Column for the Internal Population QC Report in the Subject QC Summary Tables Documentation documentation Improvements or additions to documentation easy These tasks should take <10 min good first issue Good for newcomers
#368 opened Dec 11, 2024 by jaamarks
Subject IDs Exceeding 39 Characters Lead to Truncation and Errors in agg_population_qc_tables Rule
#366 opened Dec 11, 2024 by jaamarks
Improving sample_concordance_king performance question Further information is requested
#364 opened Dec 2, 2024 by rajwanir
1
@rajwanir
2
Generate a PCA plot using all subjects passed QC
#357 opened Nov 22, 2024 by 1teaspoon
1
How to handle multi-genome build in gtc2vcf?
#348 opened Oct 18, 2024 by rajwanir
@rajwanir
Incorrect Help Message in sample_qc_table.py easy These tasks should take <10 min good first issue Good for newcomers
#340 opened Oct 1, 2024 by jaamarks
Update Snakemake from v6 to newer v8
#339 opened Oct 1, 2024 by jaamarks
1
Running tests with RealData
#329 opened Sep 26, 2024 by rajwanir
When importing bcf/vcf to plink, alleles can get flipped.
#321 opened Sep 13, 2024 by rajwanir
1
Pipeline changes with concordance for better computation time in large samples
#312 opened Aug 6, 2024 by kliao12
samples_1kg_rsID.csv is empty in qc runs of GSAv3 platform
#296 opened Jun 3, 2024 by 1teaspoon
grouped_gtc_to_bed fails when one of the GTC files are corrupted enhancement New feature or request
#293 opened May 28, 2024 by shukwong
2
Create VCF entry point enhancement New feature or request
#292 opened May 28, 2024 by carynwillis
@carynwillis
1
Add Slurm option for account to be charged for resources used enhancement New feature or request
#289 opened May 20, 2024 by jaamarks
@jaamarks
Create docker and singularity images for pipeline
#250 opened Aug 7, 2023 by dorks81
@jsanjak @n8sean
Option to run the QC pipeline with GTC files only (without the idat files)
#247 opened Jul 19, 2023 by liuj1818
Unknown sample count missing in Table 1 bug Something isn't working
#238 opened Aug 23, 2022 by 1teaspoon
@jaamarks
2
internal QC vs project QC in sample sheet
#219 opened Feb 18, 2022 by 1teaspoon
1
ProTip! Add no:assignee to see everything that’s not assigned.