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Issues list

Identify lack of scalability in gwas_linear_regression performance
#390 opened Nov 17, 2020 by eric-czech
60
Test IO on large scale data IO Issues related to reading and writing common third-party file formats performance
#48 opened Jul 16, 2020 by jeromekelleher
@jeromekelleher
25
♻️ cirun not shutting down GCE instances bug Something isn't working process + tools
#842 opened Apr 14, 2022 by ravwojdyla
19
maximise lossless compression of vcf_to_zarr
#925 opened Oct 6, 2022 by elswob
18
Genotype call array to dosage core operations Issues related to domain-specific functionality such as LD pruning, PCA, association testing, etc. data representation Issues related to how data is represented: data types, data structures, indexes, access methods, etc
#21 opened Jul 8, 2020 by alimanfoo
18
Genome region query API data representation Issues related to how data is represented: data types, data structures, indexes, access methods, etc
#25 opened Jul 8, 2020 by alimanfoo
15
Unused alleles being "" is confusing for downstream tools - consider None?
#1006 opened Jan 25, 2023 by benjeffery
12
sgkit.io.vcf.vcf_to_zarr() fails to convert VCFs with INFO/CSQ and other unbounded annotations
#1059 opened Apr 5, 2023 by tnguyengel
11
Implement gene set association analysis
#692 opened Sep 30, 2021 by eric-czech
11
gwas_tutorial.ipynb taking too long to run.
#934 opened Oct 17, 2022 by benjeffery
1
@benjeffery
10
Support macOS arm64 processors process + tools
#655 opened Aug 30, 2021 by tomwhite
10
Create a public GWAS workflow for collaborative optimization
#438 opened Jan 13, 2021 by eric-czech
10
0.3% of Sgkit and Hail's allele frequency results are different with Plink's
#753 opened Oct 28, 2021 by LiangdeLI
9
Genetics data IO performance stats/doc documentation Improvements or additions to documentation IO Issues related to reading and writing common third-party file formats performance
#437 opened Jan 12, 2021 by ravwojdyla
9
Requirements for UKB GWAS core operations Issues related to domain-specific functionality such as LD pruning, PCA, association testing, etc.
#67 opened Jul 24, 2020 by eric-czech
8 of 11 tasks
9
Add tskit as import format? enhancement New feature or request IO Issues related to reading and writing common third-party file formats question Further information is requested
#64 opened Jul 24, 2020 by jeromekelleher
9
vcf_to_zarr creates zero-sized first chunk which results in incorrect dtype. bug Something isn't working upstream Used when our build breaks due to upstream changes
#1090 opened May 18, 2023 by benjeffery 0.9.1
@benjeffery
8
Implement G123 selection statistic
#980 opened Dec 20, 2022 by sanjaynagi
8
Mean of windowed popgen stats
#662 opened Sep 9, 2021 by timothymillar
8
Possible race condition in _concat_zarrs_optimized IO Issues related to reading and writing common third-party file formats
#388 opened Nov 17, 2020 by tomwhite
8
Recommend using branches in developer's fork documentation Improvements or additions to documentation process + tools
#129 opened Aug 20, 2020 by jeromekelleher
8
MemoryError: Allocation failed (probably too large) with ped.compute()
#1213 opened Apr 8, 2024 by fouerghi
7
VCF parsing memory usage
#1168 opened Jan 11, 2024 by benjeffery
7
import sgkit takes ~1.5s
#931 opened Oct 14, 2022 by benjeffery
7
Example popgen notebook documentation Improvements or additions to documentation
#602 opened Jun 8, 2021 by tomwhite
@tomwhite
7
ProTip! Adding no:label will show everything without a label.