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

htsget

Status: Open.

#838 In samtools/hts-specs;

· brainstorm opened on Aug 6, 2025

htsget: spec should indicate (dictate?) whether .vcf.gz is preferred (mandatory?) over plaintext .vcf?

htsget

Status: Open.

#837 In samtools/hts-specs;

· brainstorm opened on Aug 6, 2025

VCF 4.4+ INV pos/reference base example

vcf

Status: Open.

#836 In samtools/hts-specs;

· davmlaw opened on Jul 21, 2025

Incorrect encoding for haploid individual in GT example

vcf

Status: Open.

#835 In samtools/hts-specs;

· daviesrob opened on Jul 15, 2025

VCF text cut off by the edge of the page

vcf

Status: Open.

#834 In samtools/hts-specs;

· daviesrob opened on Jul 15, 2025

Percent encoding is under-defined

vcf

Status: Open.

#829 In samtools/hts-specs;

· d-cameron opened on May 28, 2025

HQ is underdefined

vcf

Status: Open.

#827 In samtools/hts-specs;

· d-cameron opened on May 14, 2025

GL genotype ordering does not account for phasing

vcf

Status: Open.

#826 In samtools/hts-specs;

· d-cameron opened on May 14, 2025

VCF Specification Clarification: complex rearrangements with -/- strand partner fusions

vcf

Status: Open.

#825 In samtools/hts-specs;

· VinoVino opened on May 9, 2025

Sequence Collections in SAM headers

sam

Status: Open.

#824 In samtools/hts-specs;

· jkbonfield opened on Apr 30, 2025

VCF specs - alternative to duplicate <CNV> ALT alleles?

vcf

Status: Open.

#818 In samtools/hts-specs;

· chrchang opened on Mar 23, 2025

Discussion: can we have programmatic output as well as PDF/LaTeX?

Status: Open.

#814 In samtools/hts-specs;

· yfarjoun opened on Feb 16, 2025