NCI-CGR GwasQcPipeline issues

NCI-CGR / GwasQcPipeline

The CGR GWAS QC processing workflow.

https://nci-cgr.github.io/GwasQcPipeline/

MIT License

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issues

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report: Clarify loci filter precedence in QC_Report.docx (issue #288)

#320 jaamarks opened 16 hours ago
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fix: Handle removal of discordant expected duplicates (issue #210)

#319 jaamarks closed 16 hours ago
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GTC to VCF creating too large of file for 100K+ samples

#318 carynwillis opened 1 day ago
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enhancement: Add data dictionary for QC_Report to delivery folder (Issue #313)

#317 jaamarks closed 1 week ago
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rule sample_level_ibd needs scale up time limit and memory for large sample size (110k)

#316 1teaspoon opened 1 week ago
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rule sample_concordance_king needs scale up time limit for large sample size (110k)

#315 1teaspoon opened 2 weeks ago
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BCF entry point with intensity and contamination checks using BCF for data_catalog usage.

#314 rajwanir opened 3 weeks ago
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Create Data Dictionary for QC Report

#313 jaamarks closed 1 week ago
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Pipeline changes with concordance for better computation time in large samples

#312 kliao12 opened 1 month ago
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Update branch

#311 kliao12 closed 1 month ago
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302 skip merging graf king and plink results to make the qc pipeline more efficient

#310 kliao12 closed 1 month ago
1
Issue 222

#309 carynwillis closed 1 month ago
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high call rate chrY snps observed in genome studio are not retained in qc'ed genotype data

#308 1teaspoon opened 1 month ago
1
bugfix: retrieve additional missing data from `QC_Report.xlsx`

#307 jaamarks closed 1 month ago
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Handle Missing Data in `QC_Report.xlsx` (Follow up to #303)

#306 jaamarks closed 1 month ago
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switch snp and call rate filters

#305 kliao12 closed 2 months ago
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bugfix: `is_unexpected_replicate` data missing in `QC_Report.xlsx`

#304 jaamarks closed 1 month ago
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Empty `is_unexpected_replicate` column in QC_Report.xlsx

#303 jaamarks closed 1 month ago
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skip merging Graf, King and Plink results to make the QC pipeline more efficient

#302 shukwong closed 1 month ago
1
fix checkpoint to check populations for # controls

#301 kliao12 closed 2 months ago
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287 dynamically adjust minimum maf for hwe calculation and add option to set hwe p value threshold

#300 kliao12 closed 2 months ago
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performance: improve memory allocation for `sample_qc` subworkflow

#299 jaamarks closed 3 months ago
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refactor: update python deploy workflow

#298 jaamarks closed 3 months ago
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performance: more aggressive time scaling in `sample_qc`

#297 jaamarks closed 3 months ago
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samples_1kg_rsID.csv is empty in qc runs of GSAv3 platform

#296 1teaspoon opened 3 months ago
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Checkpoint prevents populations with >50 cases or controls but <50 cases and <50 controls running HWE

#295 kliao12 closed 2 months ago
1
graf_populations running out of memory

#294 jaamarks closed 3 months ago
1
grouped_gtc_to_bed fails when one of the GTC files are corrupted

#293 shukwong opened 3 months ago
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Create VCF entry point

#292 carynwillis opened 3 months ago
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bugfix: error when setting `case_control_gwas=true`

#291 jaamarks closed 3 months ago
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281 ancestry = unknown not shown in table 3 subject counts by ancestry group

#290 kliao12 closed 3 months ago
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Add Slurm option for account to be charged for resources used

#289 jaamarks opened 3 months ago
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call rate filter

#288 1teaspoon closed 2 months ago
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dynamically adjust minimum MAF for HWE calculation and add option to set HWE p value threshold

#287 shukwong closed 2 months ago
2
add pulp2.7.0 to pyproject.toml

#286 kliao12 closed 4 months ago
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AttributeError: module 'pulp' has no attribute 'list_solvers'

#285 shukwong closed 4 months ago
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fix empty relatedness files

#284 kliao12 closed 4 months ago
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feature: add a generic slurm cluster submit option

#283 jaamarks closed 4 months ago
2
v1.4.0 testing on 90k sample dataset: rule sample_concordance_king exceeds time limit

#282 1teaspoon closed 3 months ago
7
Ancestry = "Unknown" not shown in Table 3 Subject Counts by Ancestry Group

#281 1teaspoon opened 4 months ago
2
case_control_gwas option error: Missing input files for rule gwas

#280 1teaspoon closed 3 months ago
1
Update readme

#279 kliao12 closed 4 months ago
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Fix documentation auto implementation of version release

#278 kliao12 closed 4 months ago
1
Correct column name for analytic_exclusion

#277 carynwillis closed 4 months ago
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Correct column names for testing

#276 carynwillis closed 4 months ago
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Automatic Lims upload capability and QC table column additions

#275 carynwillis closed 4 months ago
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Issue 237

#274 kliao12 closed 4 months ago
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Issue 237, ensure ancestry plot only uses project QC, standardizing plots in QC report

#273 kliao12 closed 4 months ago
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Refactor to capture exit_status for successful runs

#272 jaamarks closed 4 months ago
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Fix memory issues for larger sample sizes

#271 jaamarks closed 5 months ago
0