Search results

<code>concordance.read</code> overloads memory by reading full table.

performance

Status: Open.

#397 In NCI-CGR/GwasQcPipeline;

· rajwanir opened on Apr 15, 2025

vcf2abf takes long time on unindexed bcf.

Status: Open.

#392 In NCI-CGR/GwasQcPipeline;

· rajwanir opened on Mar 14, 2025

Graf Computation Failure When <code>convert_gtc2bcf=true</code>

bugSomething isn't workingSomething isn't working

Status: Open.

Bug

#380 In NCI-CGR/GwasQcPipeline;

· jaamarks opened on Feb 26, 2025

Plink2 error: ALT allele code that's identical to the REF allele code.

bugSomething isn't workingSomething isn't working

Status: Open.

#369 In NCI-CGR/GwasQcPipeline;

· rajwanir opened on Jan 6, 2025

Missing Column for the Internal Population QC Report in the Subject QC Summary Tables Documentation

documentationImprovements or additions to documentationImprovements or additions to documentation

easyThese tasks should take <10 minThese tasks should take <10 min

good first issueGood for newcomersGood for newcomers

Status: Open.

#368 In NCI-CGR/GwasQcPipeline;

· jaamarks opened on Dec 11, 2024

Subject IDs Exceeding 39 Characters Lead to Truncation and Errors in <code>agg_population_qc_tables</code> Rule

Status: Open.

#366 In NCI-CGR/GwasQcPipeline;

· jaamarks opened on Dec 11, 2024

Generate a PCA plot using all subjects passed QC

Status: Open.

#357 In NCI-CGR/GwasQcPipeline;

· 1teaspoon opened on Nov 22, 2024

Incorrect Help Message in <code>sample_qc_table.py</code>

easyThese tasks should take <10 minThese tasks should take <10 min

good first issueGood for newcomersGood for newcomers

Status: Open.

#340 In NCI-CGR/GwasQcPipeline;

· jaamarks opened on Oct 1, 2024

Update Snakemake from v6 to newer v8

Status: Open.

#339 In NCI-CGR/GwasQcPipeline;

· jaamarks opened on Oct 1, 2024

Running tests with RealData

Status: Open.

#329 In NCI-CGR/GwasQcPipeline;

· rajwanir opened on Sep 26, 2024

When importing bcf/vcf to plink, alleles can get flipped.

Status: Open.

#321 In NCI-CGR/GwasQcPipeline;

· rajwanir opened on Sep 13, 2024

Pipeline changes with concordance for better computation time in large samples

Status: Open.

#312 In NCI-CGR/GwasQcPipeline;

· kliao12 opened on Aug 6, 2024