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26 Open 189 Closed
26 Open 189 Closed
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Issues list

Option to skip ancestry check. enhancement New feature or request workflow Anything related to snakemake componenets
#374 opened Jan 24, 2025 by rajwanir
@rajwanir
if not sex_chr_included skip impute_sex bug Something isn't working
#373 opened Jan 22, 2025 by rajwanir
@rajwanir
_read_GRAF fails when all samples do not have a Computed population label.
#372 opened Jan 17, 2025 by rajwanir
@rajwanir
With convert_gtc2bcf, contamination and intensity checks should be done using BCF. workflow Anything related to snakemake componenets
#371 opened Jan 14, 2025 by rajwanir
@rajwanir
Samples with missing IDAT and/or GTC with IDAT entry_point. workflow Anything related to snakemake componenets
#370 opened Jan 8, 2025 by rajwanir
@rajwanir
Plink2 error: ALT allele code that's identical to the REF allele code. bug Something isn't working
#369 opened Jan 6, 2025 by rajwanir
@rajwanir
Missing Column for the Internal Population QC Report in the Subject QC Summary Tables Documentation documentation Improvements or additions to documentation easy These tasks should take <10 min good first issue Good for newcomers
#368 opened Dec 11, 2024 by jaamarks
Subject IDs Exceeding 39 Characters Lead to Truncation and Errors in agg_population_qc_tables Rule
#366 opened Dec 11, 2024 by jaamarks
Improving sample_concordance_king performance question Further information is requested
#364 opened Dec 2, 2024 by rajwanir
1
@rajwanir
2
Defining threads via variable instead of hardcoding. CLI Command line interface submission Anything related to cluster submission
#360 opened Nov 25, 2024 by rajwanir
1
@rajwanir
Out of Memory Error with sample_concordance_plink Rule
#358 opened Nov 25, 2024 by jaamarks
@jaamarks
Generate a PCA plot using all subjects passed QC
#357 opened Nov 22, 2024 by 1teaspoon
1
How to handle multi-genome build in gtc2vcf?
#348 opened Oct 18, 2024 by rajwanir
@rajwanir
Incorrect Help Message in sample_qc_table.py easy These tasks should take <10 min good first issue Good for newcomers
#340 opened Oct 1, 2024 by jaamarks
Update Snakemake from v6 to newer v8
#339 opened Oct 1, 2024 by jaamarks
1
Running tests with RealData
#329 opened Sep 26, 2024 by rajwanir
When importing bcf/vcf to plink, alleles can get flipped.
#321 opened Sep 13, 2024 by rajwanir
1
Pipeline changes with concordance for better computation time in large samples
#312 opened Aug 6, 2024 by kliao12
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 enhancement New feature or request
#293 opened May 28, 2024 by shukwong
2
Create VCF entry point enhancement New feature or request
#292 opened May 28, 2024 by carynwillis
@carynwillis
1
Add Slurm option for account to be charged for resources used enhancement New feature or request
#289 opened May 20, 2024 by jaamarks
@jaamarks
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
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