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NCI-CGR
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GwasQcPipeline
The CGR GWAS QC processing workflow.
https://nci-cgr.github.io/GwasQcPipeline/
MIT License
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Fix memory issues for larger sample sizes
#271
jaamarks
closed
5 months ago
0
sort IBD and Family tabs in QC_Report
#270
carynwillis
closed
6 months ago
0
Unexpected Replicate count/flag when one of the pair is contaminated
#269
1teaspoon
opened
6 months ago
3
Test and debug the generic slurm cluster submit option
#268
shukwong
closed
4 months ago
0
Fixes #240: convert alt case/control labels to Unknown
#267
jaamarks
closed
6 months ago
2
Lims upload formatting
#266
carynwillis
closed
7 months ago
0
Potential Bug: Incompatibility time variable in modules/plink.smk and sub_workflows/contamination.smk
#265
jaamarks
closed
5 months ago
0
CI/CD for Automated Documentation Updates with Latest Software Version Tag
#264
jaamarks
closed
4 months ago
1
Grafpop and graf2.4 implementation
#263
kliao12
closed
7 months ago
0
Incorrect Completion Status: Workflow Completes but Logs Indicate Error
#262
shukwong
closed
5 months ago
0
create cluster profile for Cambridge HPC profile
#261
shukwong
closed
6 months ago
1
Dev/dev docs
#260
jsanjak
closed
1 year ago
0
Dev/dev docs
#259
jsanjak
closed
1 year ago
0
Pull from default
#258
jsanjak
closed
1 year ago
0
Dev/sphinx success
#257
jsanjak
closed
1 year ago
0
Update README.md
#256
jsanjak
closed
1 year ago
0
Pull updates from default
#255
jsanjak
closed
1 year ago
0
Ccad slurm2
#254
n8sean
closed
1 year ago
0
Ccad slurm2
#253
dorks81
closed
1 year ago
0
pull
#252
dorks81
closed
1 year ago
0
Create ccad2 profile
#251
dorks81
closed
1 year ago
1
Create docker and singularity images for pipeline
#250
dorks81
opened
1 year ago
0
Ccad2 slurm jss
#249
jsanjak
closed
1 year ago
0
Dev/docker test
#248
jsanjak
closed
1 year ago
0
Option to run the QC pipeline with GTC files only (without the idat files)
#247
liuj1818
opened
1 year ago
0
new graf-pop software implementation
#246
1teaspoon
closed
7 months ago
4
pipeline job submission problem on the cgems cluster
#245
1teaspoon
closed
4 months ago
1
pipeline job submission problem on the cgr slurm system
#244
1teaspoon
closed
4 months ago
1
Lims_Upload file header and low call rate column of samples missing gtcs not correct
#243
1teaspoon
closed
6 months ago
2
Unexpected dups not populated in the Unexpected Replicate column of the Lims_Upload file
#242
1teaspoon
closed
6 months ago
1
memory issue sample size above 60k
#241
1teaspoon
closed
5 months ago
7
Summary table 4a/4b: Unknown samples not counted
#240
1teaspoon
closed
6 months ago
2
modify text in template doc Section 4.5 Subject Relateness
#239
1teaspoon
closed
6 months ago
2
Unknown sample count missing in Table 1
#238
1teaspoon
opened
2 years ago
2
Unknow samples missing in the triangle plot (Figure 3)
#237
1teaspoon
closed
5 months ago
1
build(deps-dev): bump pillow from 8.4.0 to 9.0.1
#236
dependabot[bot]
closed
2 years ago
0
Add feature to use both case and controls if number of cases is less than 50 for HWE plot
#235
dorks81
closed
1 year ago
1
Change df.append(record) to pd.concat() in sample_concordance.py file
#234
dorks81
closed
2 years ago
1
Please look into dependabot critical issues
#233
shukwong
closed
2 years ago
2
create documentation on running the pipeline using a slurm cluster on GCP
#232
shukwong
opened
2 years ago
0
Update snakemake version to 6.15.5 in pyproject.toml
#231
dorks81
closed
2 years ago
1
Create installation documentation for Slurm cluster
#230
shukwong
closed
3 months ago
0
QC report template has a typo
#229
liuj1818
closed
1 year ago
1
LIMS upload function needs to be tested
#228
liuj1818
closed
5 months ago
3
Need updates/improvements for "Sample_QC" sheet of the QC summary excel file
#227
liuj1818
closed
5 months ago
2
Adding a Illumina manifest file file in the delivery folder
#226
liuj1818
closed
2 years ago
1
Snakemake version
#225
FrederickDong
closed
2 years ago
2
Conda environment error during pipeline execution
#224
FrederickDong
closed
2 years ago
0
Cannot run cgr command on GCP after installation on 3/11/2022
#223
FrederickDong
closed
2 years ago
2
gtc to ped, 0|G is actually A|G
#222
1teaspoon
closed
1 month ago
0
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