Issues

• Fix build with latest htslib

  brentp/cyvcf2#336 · Filter by author tillea opened on Sep 21, 2026

• gt_bases uses inconsistent phasing separator for phased genotypes with missing alleles

  brentp/cyvcf2#331 · Filter by author juliendiot42 opened on Aug 10, 2026

• unexpected generator: vcf(), listing all variants.

  brentp/cyvcf2#324 · Filter by author hexylena opened on Feb 17, 2026

• empty string instead of boolean value when no "=" in the INFO field

  brentp/cyvcf2#314 · Filter by author no7ren opened on Apr 3, 2025
  3

• raw_header is a bit cooked

  brentp/cyvcf2#312 · Filter by author davmlaw opened on Dec 19, 2024
  4

• Return sparse representation for genotype

  brentp/cyvcf2#310 · Filter by author quattro opened on Aug 30, 2024

• record.FILTER vs. record.FILTERS

  brentp/cyvcf2#309 · Filter by author jaime11 opened on Aug 1, 2024
  1

• Skip the warnings?

  brentp/cyvcf2#303 · Filter by author AugustinMro opened on Apr 10, 2024
  2

• ##INFO fields being dropped

  brentp/cyvcf2#302 · Filter by author FlexLuthORF opened on Mar 13, 2024
  6

• Adding new variant record

  brentp/cyvcf2#299 · Filter by author LindoNkambule opened on Feb 11, 2024

• No macOS arm64 wheels available for 0.30.26 and 0.30.27

  brentp/cyvcf2#297 · Filter by author bruggsy opened on Jan 29, 2024
  1

• Crash with single GT allele value - UnicodeDecodeError: 'ascii' codec can't decode byte 0x81 in position 1: ordinal not in range(128)

  brentp/cyvcf2#291 · Filter by author davmlaw opened on Dec 22, 2023
  2

• Any method available to split vcf files into individual sample vcf files

  brentp/cyvcf2#284 · Filter by author raghvendra44 opened on Nov 29, 2023

• Streaming VCFs using smart_open?

  brentp/cyvcf2#260 · Filter by author dbrami opened on Jan 6, 2023
  3

• Windows 11 Installing Issue

  brentp/cyvcf2#243 · Filter by author genewater opened on May 23, 2022
  6

• Can't install from source

  brentp/cyvcf2#240 · Filter by author dprat opened on May 9, 2022
  5

• Vulnerable shared libraries might make cyvcf2 vulnerable. Can you help upgrade to patch versions?

  brentp/cyvcf2#239 · Filter by author MikeWazoWski123 opened on Apr 1, 2022
  3

• Issue querying db's made with latest cyvcf2

  brentp/cyvcf2#238 · Filter by author matthdsm opened on Mar 29, 2022
  5

• is_indel treats "<NON_REF>" ALT as an indel

  brentp/cyvcf2#217 · Filter by author vsbuffalo opened on Jul 27, 2021
  3

• Can't read remote VCF files over https on Linux

  brentp/cyvcf2#216 · Filter by author tomwhite opened on Jul 21, 2021

• cannot import name 'VCF' from 'cyvcf2' (unknown location)

  brentp/cyvcf2#201 · Filter by author LDHHAHA opened on May 21, 2021
  2

• No error thrown with an invalid region

  brentp/cyvcf2#200 · Filter by author jamespeapen opened on May 5, 2021

• Return missing values mask for Integer INFO/FORMAT fields

  brentp/cyvcf2#195 · Filter by author tomwhite opened on Mar 9, 2021
  2

• Copy header from one VCF to another

  brentp/cyvcf2#194 · Filter by author multimeric opened on Mar 8, 2021
  1

• INFO property for Variant class

  brentp/cyvcf2#192 · Filter by author hammer opened on Feb 14, 2021
  4