Issues

• Make sample_filter_pass an optional pseudofield like variant_index

  sgkit-dev/vcztools#374 · Filter by author jeromekelleher opened on May 13, 2026

• view -e EXPR diverges from bcftools when EXPR is pure sample-scope (FMT/...)

  Bug

  sgkit-dev/vcztools#341 · Filter by author jeromekelleher opened on May 6, 2026

• AttributeError: 'slice' object has no attribute 'size'

  Bug

  sgkit-dev/vcztools#334 · Filter by author tomwhite opened on May 6, 2026
  2

• Performance on call_ field filtering is poor

  sgkit-dev/vcztools#321 · Filter by author jeromekelleher opened on Apr 28, 2026

• Test warnings

  sgkit-dev/vcztools#302 · Filter by author jeromekelleher opened on Apr 21, 2026

• bare flag identifier as the whole predicate

  Bug

  sgkit-dev/vcztools#300 · Filter by author jeromekelleher opened on Apr 20, 2026

• Complement-targeted regions fail on Windows + Python 3.11 (pyranges/sorted_nearest dtype bug)

  sgkit-dev/vcztools#290 · Filter by author jeromekelleher opened on Apr 17, 2026
  1

• Bug in VCF output when selected samples have all missing GTs.

  bug
  sgkit-dev/vcztools#289 · Filter by author jeromekelleher opened on Apr 16, 2026 · 0.2.1
  2

• Error message when decompressing .vcz data with vcztools

  sgkit-dev/vcztools#245 · Filter by author browning-lab opened on Dec 15, 2025
  11

• Document example of outputting to compressed VCF

  sgkit-dev/vcztools#244 · Filter by author hyanwong opened on Oct 30, 2025
  4

• Support higher dimensional FORMAT fields in filtering expressions

  sgkit-dev/vcztools#232 · Filter by author tomwhite opened on Jun 9, 2025

• Support multiallelic sites in plink

  enhancement
  sgkit-dev/vcztools#224 · Filter by author jeromekelleher opened on May 28, 2025

• Add conda package

  sgkit-dev/vcztools#219 · Filter by author jeromekelleher opened on May 27, 2025
  1

• Handling Zero-ploidy individuals in the output

  sgkit-dev/vcztools#212 · Filter by author jeromekelleher opened on May 16, 2025

• Add OpenTelemetry support?

  enhancement
  sgkit-dev/vcztools#196 · Filter by author jeromekelleher opened on Apr 7, 2025
  1

• Functions not supported in query

  sgkit-dev/vcztools#192 · Filter by author jeromekelleher opened on Apr 4, 2025

• Automatic variables not supported in query

  sgkit-dev/vcztools#191 · Filter by author jeromekelleher opened on Apr 4, 2025
  1

• All functions unsupported in filtering query language

  sgkit-dev/vcztools#190 · Filter by author jeromekelleher opened on Apr 4, 2025

• Add modulo support for filter arithmetic

  enhancement
  sgkit-dev/vcztools#185 · Filter by author jeromekelleher opened on Apr 3, 2025

• Improve error messages from filter expression parsing

  sgkit-dev/vcztools#183 · Filter by author jeromekelleher opened on Apr 3, 2025
  1

• File access not supported in filtering

  sgkit-dev/vcztools#175 · Filter by author jeromekelleher opened on Apr 2, 2025

• Regex operators not supported in filtering

  sgkit-dev/vcztools#174 · Filter by author jeromekelleher opened on Apr 2, 2025

• Number/fraction of samples passing function not supported in filtering

  sgkit-dev/vcztools#172 · Filter by author jeromekelleher opened on Apr 2, 2025

• Default variables not supported in filtering

  sgkit-dev/vcztools#171 · Filter by author jeromekelleher opened on Apr 2, 2025

• Binomial and Fisher tests not supported in filtering

  sgkit-dev/vcztools#170 · Filter by author jeromekelleher opened on Apr 2, 2025