samtools/hts-specs

Issues

• [Improvement] BAM file format, optional strandedness field in header for RNA-seq

  #787 opened 8 days ago by rLannes
  6

• cram: interpretation of "unmapped" flag in a pseudocode seems incorrect

  #749 opened 9 days ago by athos
  2

• 0-based coordinate system error in sam spec?

  #786 opened 19 days ago by jacobscgc
  2

• MM tag preferred format for TAPS data

  #785 opened 22 days ago by jamesbaye
  0

• INFO/END should not be deprecated

  #784 opened a month ago by pd3
  14

• BED "chrom" field regex is inconsistent with existing practice

  #779 opened 2 months ago by EricR86
  5

• Number, type and description on FORMAT not in sync with List of changes

  #777 opened 2 months ago by vasudeva8
  0

• FORMAT field CICN and its relation to CN field

  #778 opened 2 months ago by vasudeva8
  0

• INFO CIPOS Number=2xA

  #783 opened a month ago by rkimoakbioinformatics
  0

• VCF4.4 SVLEN requirement across different variant representations

  #769 opened 4 months ago by tcezard
  6

• Using ChaCha20-Poly1305 for encryption is NOT FIPS140-3 compliant and not justified and is considered unprotected plaintext

  #780 opened a month ago by mmokrejs
  3

• vcf: VCF 4.5 gVCF example has off-by-one errors

  #781 opened a month ago by zaeleus
  0

• How to retrieve the primary alignment for secondary and supplementary reads

  #755 opened 2 months ago by nh13
  9

• VCF Draft 4.5 and Modified Bases

  #767 opened 5 months ago by cjw85
  29

• VCF format: correct representation of complex indels and MNPs

  #774 opened 3 months ago by marc-sturm
  5

• vcf: Invalid unstructured header line in VCF 4.3 example `complexfile_passed_000.vcf`

  #772 opened 3 months ago by zaeleus
  2

• vcf: Handling structured header records with missing IDs in VCF 4.1/4.2

  #760 opened 3 months ago by zaeleus
  1

• Is there a semantic difference between GT=./. and GT=0/0 + GQ=0 ?

  #756 opened 3 months ago by yfarjoun
  15

• vcf: Failed example has irrelevant error

  #717 opened 3 months ago by zaeleus
  1

• refget: v2 spec for Range header errors does not align with typical usage

  #771 opened 3 months ago by davidlougheed
  0

• Questions about third-party use of test data

  #766 opened 5 months ago by athos
  6

• bcf: First phasing indicators not set in genotype (GT) value examples

  #762 opened 5 months ago by zaeleus
  0

• VCF: "Genotype fields" vs "FORMAT" and per-sample

  #738 opened 5 months ago by jkbonfield
  1

• test/vcf: Duplicate contig header record ID

  #744 opened 5 months ago by zaeleus
  0

• CSI file is BGZF compressed but this is not mentioned in the CSV1 spec

  #765 opened 5 months ago by bguo068
  2

• cram: Inconsistent descriptions of auxiliary tag types

  #757 opened 6 months ago by athos
  1

• sam-tags: `MM` field value pattern does not allow ambiguity codes

  #732 opened a year ago by zaeleus
  3

• SA tag CIGAR format

  #759 opened 6 months ago by jo-mc
  0

• test/sam: Duplicate aux field tags

  #742 opened 7 months ago by zaeleus
  0

• CRAM: Need to improve feature positions description

  #747 opened 7 months ago by daviesrob
  1

• Modified base single letter codes update

  #741 opened 7 months ago by marcus1487
  7

• SVCLAIM: VCF4.4 and backward compatibility with VCF4.3

  #750 opened 7 months ago by tcezard
  1

• is `*` better than `\*`?

  #748 opened 9 months ago by zhitian-wu
  1

• FAIRsharing Record Query - BED format

  #746 opened 10 months ago by allysonlister
  0

• primary, secondary, and supplementary alignments with optional MM tags

  #739 opened a year ago by RichardCorbett
  5

• What does `.` mean for an `A`, `R`, or `G` indexed field?

  #737 opened a year ago by danking
  6

• register bgzip in IANA media types?

  #734 opened a year ago by vidboda
  5

• Can ML Tags be zero length arrays?

  #728 opened a year ago by gileshall
  5

• Consider 64-bit values in BCF, BAM and CRAM

  #735 opened a year ago by jkbonfield
  2

• sam: Consider recommending using 0 for mapping quality when record is unmapped

  #727 opened a year ago by zaeleus
  3

• Circular chromosomes in the VCF header

  #733 opened a year ago by nh13
  1

• VCF test case filenames should be more meaningful

  #730 opened a year ago by d-cameron
  1

• sam: Define format of read group predicted median insert size

  #720 opened a year ago by zaeleus
  2

• sam: Irrelevant test failure in `aux.fail-f1.sam`

  #722 opened a year ago by zaeleus
  1

• sam: Clarify the usage of UTF-8 characters in header

  #719 opened a year ago by zaeleus
  3

• sam: Consider more conventional format versioning

  #725 opened a year ago by zaeleus
  6

• vcf: Failed filter names should disallow "PASS" and MISSING

  #716 opened a year ago by zaeleus
  1

• sam: Add PL value "MGIG400" as seen in the wild

  #718 opened a year ago by brainstorm
  5

• sam: Quality score ambiguity when sequence is a single base

  #715 opened a year ago by zaeleus
  2

• bam: Explain the use-case of the reference information section

  #713 opened a year ago by zaeleus
  2