Issues

• delete upstream workflow

  sgkit-dev/sgkit#1351 · Filter by author jeromekelleher opened on Sep 10, 2026
  3

• Error trying to get Fst for window_by_position

  sgkit-dev/sgkit#1343 · Filter by author alxsimon opened on Aug 19, 2026
  4

• Remove chunks hack

  sgkit-dev/sgkit#1342 · Filter by author hyanwong opened on May 4, 2026

• Unpin xarray

  upstream
  sgkit-dev/sgkit#1337 · Filter by author tomwhite opened on Dec 22, 2025

• missing submodules in install

  sgkit-dev/sgkit#1334 · Filter by author alxsimon opened on Sep 7, 2025

• Dead link

  sgkit-dev/sgkit#1332 · Filter by author mattlyonofh opened on Sep 1, 2025
  3

• Remove (c)bgen dependency for unpack_variables?

  sgkit-dev/sgkit#1331 · Filter by author jpfeuffer opened on Aug 6, 2025
  5

• Support bcftools-style filtering

  core operations
  sgkit-dev/sgkit#1329 · Filter by author tomwhite opened on Jul 1, 2025

• Unpin scipy when statsmodels>0.14.4 is released

  upstream
  sgkit-dev/sgkit#1323 · Filter by author tomwhite opened on Jun 24, 2025

• Incorrect allele ordering in plink

  sgkit-dev/sgkit#1315 · Filter by author jeromekelleher opened on May 20, 2025

• read_plink returns 'nan' strings for sample_ids

  bug
  sgkit-dev/sgkit#1314 · Filter by author jeromekelleher opened on May 20, 2025

• Support lazy save_dataset ?

  sgkit-dev/sgkit#1298 · Filter by author rajwanir opened on Mar 31, 2025

• The best way to append samples to a dataset?

  sgkit-dev/sgkit#1295 · Filter by author rajwanir opened on Mar 26, 2025
  2

• Citation

  sgkit-dev/sgkit#1293 · Filter by author fouerghi opened on Mar 12, 2025
  4

• Add separate function for Watterson's theta

  sgkit-dev/sgkit#1279 · Filter by author percyfal opened on Dec 5, 2024
  3

• Diversity calculations on windowed datasets generate lots of unmanaged memory

  sgkit-dev/sgkit#1278 · Filter by author percyfal opened on Dec 5, 2024
  10

• Windowing fails for datasets where contigs lack variant sites

  bug
  sgkit-dev/sgkit#1268 · Filter by author percyfal opened on Oct 10, 2024
  5

• Dask 2024.8.1 and later is very slow

  performanceupstream
  sgkit-dev/sgkit#1267 · Filter by author tomwhite opened on Oct 7, 2024
  8

• Unclear how to overwrite a dataset

  sgkit-dev/sgkit#1243 · Filter by author hyanwong opened on Jul 26, 2024
  2

• No page at https://sgkit-dev.github.io

  sgkit-dev/sgkit#1242 · Filter by author hyanwong opened on Jul 26, 2024

• Displaying alleles when using sgkit.display_genotypes(ds)

  sgkit-dev/sgkit#1240 · Filter by author hyanwong opened on Jul 25, 2024

• Update docs to say "Scalable genetics toolkit"

  sgkit-dev/sgkit#1223 · Filter by author jeromekelleher opened on Jun 7, 2024

• simulate_genotype_call_dataset creates alleles as byte strings

  bug
  sgkit-dev/sgkit#1222 · Filter by author hyanwong opened on Jun 7, 2024
  1

• simulate_genotype_call_dataset creates duplicate alleles

  bug
  sgkit-dev/sgkit#1221 · Filter by author hyanwong opened on Jun 7, 2024

• Genome accessibility/callability

  sgkit-dev/sgkit#1219 · Filter by author mufernando opened on May 22, 2024
  4