Resubmission checklist

[jeromekelleher]

Checklist for things that need to be done in time for the submission deadline 2025-01-31 (or, for parts of the software ecosystem, things that need to be good-as done and completed within a few days).

Local alleles

• Discuss our implementation of local alleles. xref: Add discussion of local alleles #187 Update local alleles paper #186 and LPL no smaller than PL bio2zarr#277
• Complete implementation in bio2zarr Finalise details of local alleles implementation bio2zarr#298

Write up GEL S3 experiments

• Add some paragraphs to the end of the GEL section describing experiments done. See S3 notebooks here https://github.com/sgkit-dev/vcf-zarr-publication/tree/main/gel_example . xref Update GEL benchmarks to also report performance on S3 #174
• Add supplemental figs Supplemental fig(s) for S3 benchmarks #188
• Relevant: Note that highest compression levels are not useful in cloud storage #182 Cite Exploiting Cloud Object Storage for High-Performance Analytics #181

Finish Norway spruce example

Initial issue: #169

• Rerun conversion to use updated local alleles code Revise Spruce section to use local alleles implementation #189. Waiting on Finalise details of local alleles implementation bio2zarr#298
• Check discussion of VCF chr length accuracy Ensure discussion on VCF position is correct #180

Our Future Health case study

• Our Future Health case study #190

All of us case study

• All of Us case study #191

SARS-CoV-2 case study

• Add a case study on Viridian SARS-Cov-2 data? #172

SAIGE prototype

• Add section discussing SAIGE prototype #173

VCZtools

• Add section for vcztools #192

Additional afdist Zarr implementations

• Additional afdist implementation benchmarks #194