Issues

• Revision of BAM specification for zstd block compression and BAM-specific pain points

  samtools/hts-specs#876 · Filter by author tfenne opened on Nov 3, 2026
  1

• Missing information in QUERY/POST table compared to GET

  htsget
  samtools/hts-specs#875 · Filter by author jmarshall opened on Oct 20, 2026

• Pan-genome alignment to sequence missing from the linear reference.

  samtools/hts-specs#873 · Filter by author d-cameron opened on Oct 6, 2026
  12

• SAM Spec Suggestion: VX:i optional tag

  samsam-tags
  samtools/hts-specs#872 · Filter by author pdimens opened on Sep 23, 2026
  9

• VCFv4.5/4.4 Specification Inaccuracy -- Genotype Fields [§1.6.2]

  vcf
  samtools/hts-specs#871 · Filter by author ecrum19 opened on Sep 11, 2026
  1

• VCFv4.5 Specification Typo -- Tandem Repeats [§5.7]

  samtools/hts-specs#870 · Filter by author ecrum19 opened on Sep 11, 2026
  1

• VCFv4.5 Specification Inaccuracy -- Large Insertions (Circular) [§5.4.2]

  samtools/hts-specs#869 · Filter by author ecrum19 opened on Sep 11, 2026

• Examples using Number=P and/or PSL/PSO/PSQ fields

  vcf
  samtools/hts-specs#868 · Filter by author jmarshall opened on Sep 6, 2026

• cram: Clarify whether tag ID lists are separated or terminated

  cram
  samtools/hts-specs#867 · Filter by author zaeleus opened on Aug 25, 2026

• Allow http QUERY method in htsget

  htsget
  samtools/hts-specs#866 · Filter by author jmarshall opened on Aug 25, 2026
  1

• The meaning of an "optional field" VCF and a clash with ##contig

  vcf
  samtools/hts-specs#865 · Filter by author jkbonfield opened on Aug 13, 2026
  2

• Recommended practice "No alignments should be assigned mapping quality 255" is ambiguous

  sam
  samtools/hts-specs#864 · Filter by author jmarshall opened on Aug 11, 2026
  2

• EVENTTYPE can be different for records with the same EVENT

  vcf
  samtools/hts-specs#863 · Filter by author d-cameron opened on Aug 10, 2026

• Error in VCF test files

  samtools/hts-specs#860 · Filter by author markwoon opened on Jul 25, 2026

• rlen calculation in bcf/vcf

  vcf
  samtools/hts-specs#857 · Filter by author vasudeva8 opened on May 29, 2026

• ITF-8/LTF-8 spec text has typos, an incorrect prefix description, and lacks examples

  samtools/hts-specs#855 · Filter by author yfarjoun opened on Mar 31, 2026
  4

• Missing value for SVCLAIM in DEL/DUP in VCFv4.4: clarification and addition

  vcf
  samtools/hts-specs#849 · Filter by author khetherin opened on Jan 19, 2026
  1

• Is the set of ##ALT top-level types in IDs *really* restricted to the 5 provided?

  vcf
  samtools/hts-specs#848 · Filter by author adamnovak opened on Jan 15, 2026

• how to index a read in a circular sequence?

  sam
  samtools/hts-specs#847 · Filter by author yfarjoun opened on Dec 18, 2025
  1

• A molecular-annotation-spec for SAM/BAM/CRAM with new reserved tags

  samsam-tags
  samtools/hts-specs#846 · Filter by author mrvollger opened on Nov 20, 2025
  4

• Fix explaination of BS data series in CRAM

  cram
  samtools/hts-specs#845 · Filter by author jkbonfield opened on Oct 23, 2025
  

• TLEN meaning when leftmost and rightmost are the same for a pair, or the same for a single record

  cramsam
  samtools/hts-specs#842 · Filter by author jkbonfield opened on Sep 3, 2025
  3

• htsget: using htsget server to mask regions from users (i.e clinical usecase(s))

  htsget
  samtools/hts-specs#838 · Filter by author brainstorm opened on Aug 6, 2025
  2

• Incorrect encoding for haploid individual in GT example

  vcf
  samtools/hts-specs#835 · Filter by author daviesrob opened on Jul 15, 2025

• VCF text cut off by the edge of the page

  vcf
  samtools/hts-specs#834 · Filter by author daviesrob opened on Jul 15, 2025