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19 Open 174 Closed
19 Open 174 Closed
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Issues list

Hi Sam, Thank you for the tool and pipeline, since pigs_calc provide the SUM and three ansectry correction including Z_MostSimilarPop, Z_norm1, and Z_norm2, which of these scores is the most accurate to use in the further analyses, and do these ancestry normalization control for PGS confounders including the population stratification, or do we still need to use the top 10 PCs in the statistical analyses. Thank you.
#385 opened Oct 25, 2024 by SalemWerdyani
The error of MATCH_VARIANTS in profile test user-query User queries & requests
#383 opened Oct 14, 2024 by yambirj
1
Better matching of INDEL variants enhancement New feature or request
#377 opened Sep 30, 2024 by smlmbrt
Nextflow pipeline fails due to missing .pgen file, despite file being present. bug Something isn't working
#373 opened Sep 12, 2024 by Fiwx
1
Update ancestry doc page documentation Improvements or additions to documentation
#371 opened Sep 11, 2024 by smlmbrt
Make reports shareable by default enhancement New feature or request
#367 opened Sep 2, 2024 by nebfield
2
3
Remove defaults channel from conda profile enhancement New feature or request
#366 opened Sep 2, 2024 by nebfield
1
v2.0.0-beta.3 run: failed to find loop device, then --resume results in Failed to invoke observer completion handler (NullPointerException in BcoRenderer) bug Something isn't working user-query User queries & requests
#362 opened Aug 23, 2024 by Fiwx
@nebfield
9
matched_variants.txt.gz empty when pgsc_calc is ran with many scores, resulting in KeyError: 'CHR:POS:A0:A1' and pgscatalog-intersect failure. bug Something isn't working user-query User queries & requests
#361 opened Aug 13, 2024 by Fiwx
@nebfield
9
Improving information about PGS Catalog scoring file versions enhancement New feature or request user-query User queries & requests
#348 opened Jul 31, 2024 by mglev1n
1
Improve PGS distribution plots in report for low sample numbers enhancement New feature or request
#345 opened Jul 31, 2024 by smlmbrt
1
Scoring for non-additive models that aren't dominant/recessive bug Something isn't working enhancement New feature or request
#314 opened Jun 14, 2024 by smlmbrt
1
ToDo: test case with single sample enhancement New feature or request
#287 opened Apr 25, 2024 by smlmbrt
Improve gnomAD reference panel (HGDP+1kG) documentation Improvements or additions to documentation enhancement New feature or request
#183 opened Sep 28, 2023 by smlmbrt
2 of 4 tasks
@smlmbrt
Reference creation: current docs/code doesn't support other data bug Something isn't working documentation Improvements or additions to documentation
#164 opened Sep 7, 2023 by smlmbrt
1
Improvements to PCA steps & default reference panel enhancement New feature or request
#133 opened Jul 31, 2023 by smlmbrt
1 of 3 tasks
@smlmbrt @joeltg10
1
Integrate OmicsPred enhancement New feature or request
#99 opened Mar 30, 2023 by smlmbrt
1
Allow combined scorefiles as input documentation Improvements or additions to documentation enhancement New feature or request
#64 opened Nov 15, 2022 by smlmbrt
1
Enhance Sample and Variant-level QC enhancement New feature or request
#21 opened Mar 21, 2022 by smlmbrt
1 task done
3
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