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14 Open 164 Closed
14 Open 164 Closed
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Issues list

high call rate chrY snps observed in genome studio are not retained in qc'ed genotype data
#308 opened Jul 16, 2024 by 1teaspoon
skip merging Graf, King and Plink results to make the QC pipeline more efficient enhancement New feature or request Priority1
#302 opened Jun 16, 2024 by shukwong
@kliao12 @carynwillis
1
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
#293 opened May 28, 2024 by shukwong
Create VCF entry point enhancement New feature or request
#292 opened May 28, 2024 by carynwillis
@carynwillis
Add Slurm option for account to be charged for resources used enhancement New feature or request
#289 opened May 20, 2024 by jaamarks
@jaamarks
Unexpected Replicate count/flag when one of the pair is contaminated Priority1
#269 opened Mar 7, 2024 by 1teaspoon
@jaamarks @carynwillis
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
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
gtc to ped, 0|G is actually A|G Priority1
#222 opened Mar 2, 2022 by 1teaspoon
@carynwillis
internal QC vs project QC in sample sheet
#219 opened Feb 18, 2022 by 1teaspoon
1
required output file .nosex bug Something isn't working Priority2
#214 opened Dec 6, 2021 by 1teaspoon
@carynwillis
2
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