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Issues: NCI-CGR/GwasQcPipeline
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Discordant expected dup removal - only apply to replicates pass call rate & contamination
#324
opened Sep 19, 2024 by
1teaspoon
rule sample_level_ibd needs scale up time limit and memory for large sample size (110k)
#316
opened Aug 24, 2024 by
1teaspoon
rule sample_concordance_king needs scale up time limit for large sample size (110k)
#315
opened Aug 22, 2024 by
1teaspoon
Pipeline changes with concordance for better computation time in large samples
#312
opened Aug 6, 2024 by
kliao12
high call rate chrY snps observed in genome studio are not retained in qc'ed genotype data
#308
opened Jul 16, 2024 by
1teaspoon
grouped_gtc_to_bed fails when one of the GTC files are corrupted
#293
opened May 28, 2024 by
shukwong
Add Slurm option for account to be charged for resources used
enhancement
New feature or request
#289
opened May 20, 2024 by
jaamarks
Ancestry = "Unknown" not shown in Table 3 Subject Counts by Ancestry Group
Priority1
#281
opened Apr 30, 2024 by
1teaspoon
Unexpected Replicate count/flag when one of the pair is contaminated
Priority1
#269
opened Mar 7, 2024 by
1teaspoon
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
create documentation on running the pipeline using a slurm cluster on GCP
documentation
Improvements or additions to documentation
#232
opened Jun 15, 2022 by
shukwong
required output file .nosex
bug
Something isn't working
Priority2
#214
opened Dec 6, 2021 by
1teaspoon
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