NCI-CGR/GwasQcPipeline

Issues

• Create Data Dictionary for QC Report

  #313 opened a month ago by jaamarks
  0

• Unexpected Replicate count/flag when one of the pair is contaminated

  #269 opened 6 months ago by 1teaspoon
  3

• Pipeline changes with concordance for better computation time in large samples

  #312 opened a month ago by kliao12
  0

• skip merging Graf, King and Plink results to make the QC pipeline more efficient

  #302 opened a month ago by shukwong
  1

• high call rate chrY snps observed in genome studio are not retained in qc'ed genotype data

  #308 opened 2 months ago by 1teaspoon
  1

• Handle Missing Data in `QC_Report.xlsx` (Follow up to #303)

  #306 opened 2 months ago by jaamarks
  0

• Empty `is_unexpected_replicate` column in QC_Report.xlsx

  #303 opened 2 months ago by jaamarks
  0

• call rate filter

  #288 opened 2 months ago by 1teaspoon
  0

• Checkpoint prevents populations with >50 cases or controls but <50 cases and <50 controls running HWE

  #295 opened 3 months ago by kliao12
  1

• dynamically adjust minimum MAF for HWE calculation and add option to set HWE p value threshold

  #287 opened 3 months ago by shukwong
  2

• Create installation documentation for Slurm cluster

  #230 opened 3 months ago by shukwong
  0

• case_control_gwas option error: Missing input files for rule gwas

  #280 opened 3 months ago by 1teaspoon
  1

• v1.4.0 testing on 90k sample dataset: rule sample_concordance_king exceeds time limit

  #282 opened 3 months ago by 1teaspoon
  7

• graf_populations running out of memory

  #294 opened 3 months ago by jaamarks
  1

• samples_1kg_rsID.csv is empty in qc runs of GSAv3 platform

  #296 opened 3 months ago by 1teaspoon
  0

• grouped_gtc_to_bed fails when one of the GTC files are corrupted

  #293 opened 4 months ago by shukwong
  0

• Create VCF entry point

  #292 opened 4 months ago by carynwillis
  0

• Ancestry = "Unknown" not shown in Table 3 Subject Counts by Ancestry Group

  #281 opened 4 months ago by 1teaspoon
  1

• Add Slurm option for account to be charged for resources used

  #289 opened 4 months ago by jaamarks
  0

• Unknown sample count missing in Table 1

  #238 opened 2 years ago by 1teaspoon
  2

• AttributeError: module 'pulp' has no attribute 'list_solvers'

  #285 opened 4 months ago by shukwong
  0

• Test and debug the generic slurm cluster submit option

  #268 opened 5 months ago by shukwong
  0

• Create docker and singularity images for pipeline

  #250 opened a year ago by dorks81
  0

• pipeline job submission problem on the cgr slurm system

  #244 opened 5 months ago by 1teaspoon
  1

• pipeline job submission problem on the cgems cluster

  #245 opened 5 months ago by 1teaspoon
  1

• CI/CD for Automated Documentation Updates with Latest Software Version Tag

  #264 opened 5 months ago by jaamarks
  1

• Need updates/improvements for "Sample_QC" sheet of the QC summary excel file

  #227 opened 5 months ago by liuj1818
  2

• LIMS upload function needs to be tested

  #228 opened 5 months ago by liuj1818
  3

• Unknow samples missing in the triangle plot (Figure 3)

  #237 opened 5 months ago by 1teaspoon
  1

• Incorrect Completion Status: Workflow Completes but Logs Indicate Error

  #262 opened 5 months ago by shukwong
  0

• Potential Bug: Incompatibility time variable in modules/plink.smk and sub_workflows/contamination.smk

  #265 opened 6 months ago by jaamarks
  0

• memory issue sample size above 60k

  #241 opened 6 months ago by 1teaspoon
  7

• Summary table 4a/4b: Unknown samples not counted

  #240 opened 6 months ago by 1teaspoon
  2

• create cluster profile for Cambridge HPC profile

  #261 opened 6 months ago by shukwong
  1

• Unexpected dups not populated in the Unexpected Replicate column of the Lims_Upload file

  #242 opened 6 months ago by 1teaspoon
  1

• Lims_Upload file header and low call rate column of samples missing gtcs not correct

  #243 opened 6 months ago by 1teaspoon
  2

• modify text in template doc Section 4.5 Subject Relateness

  #239 opened 7 months ago by 1teaspoon
  2

• new graf-pop software implementation

  #246 opened 7 months ago by 1teaspoon
  4

• Create ccad2 profile

  #251 opened a year ago by dorks81
  1

• Option to run the QC pipeline with GTC files only (without the idat files)

  #247 opened a year ago by liuj1818
  0

• QC report template has a typo

  #229 opened 2 years ago by liuj1818
  1

• Add feature to use both case and controls if number of cases is less than 50 for HWE plot

  #235 opened 2 years ago by dorks81
  1

• create documentation on running the pipeline using a slurm cluster on GCP

  #232 opened 2 years ago by shukwong
  0

• Please look into dependabot critical issues

  #233 opened 2 years ago by shukwong
  2

• Adding a Illumina manifest file file in the delivery folder

  #226 opened 2 years ago by liuj1818
  1

• Change df.append(record) to pd.concat() in sample_concordance.py file

  #234 opened 2 years ago by dorks81
  1

• Cannot run cgr command on GCP after installation on 3/11/2022

  #223 opened 2 years ago by FrederickDong
  2

• Conda environment error during pipeline execution

  #224 opened 2 years ago by FrederickDong
  0

• Snakemake version

  #225 opened 2 years ago by FrederickDong
  2

• Update snakemake version to 6.15.5 in pyproject.toml

  #231 opened 2 years ago by dorks81
  1