Skip to content

Issues: samtools/hts-specs

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

175 Open 260 Closed
175 Open 260 Closed
Author
Filter by author
Loading
Label
Filter by label
Loading
Use alt + click/return to exclude labels
or ⇧ + click/return for logical OR
Projects
Filter by project
Loading
Milestones
Filter by milestone
Loading
Assignee
Filter by who’s assigned
Sort
Sort by
Newest Oldest Most commented Least commented Recently updated Least recently updated Best match
Most reactions
👍 👎 😄 🎉 😕 ❤️ 🚀 👀

Issues list

Modify SAM spec document to better represent restrictions in the SEQ field sam
#800 opened Oct 31, 2024 by Psy-Fer
4
Represent U in SAM rather than T for reads from RNA sam
#801 opened Oct 31, 2024 by Psy-Fer
12
Somewhat unclear references to types in SAMtags sam sam-tags
#798 opened Oct 14, 2024 by cmdcolin
@jkbonfield
1
Redefine GQ vcf
#797 opened Oct 10, 2024 by d-cameron
3
VCFv4.5 gVCF example malformed bug vcf
#791 opened Sep 15, 2024 by d-cameron
@d-cameron
LGL and LGP type incorrect bug vcf
#790 opened Sep 15, 2024 by d-cameron
@d-cameron
MM tag preferred format for TAPS data sam sam-tags
#785 opened Aug 22, 2024 by jamesbaye
1
@jkbonfield
1
INFO/END should not be deprecated vcf
#784 opened Aug 12, 2024 by pd3
14
INFO CIPOS Number=2xA vcf
#783 opened Aug 10, 2024 by rkimoakbioinformatics
vcf: VCF 4.5 gVCF example has off-by-one errors vcf
#781 opened Aug 8, 2024 by zaeleus
Using ChaCha20-Poly1305 for encryption is NOT FIPS140-3 compliant and not justified and is considered unprotected plaintext crypt4gh
#780 opened Aug 7, 2024 by mmokrejs
3
BED "chrom" field regex is inconsistent with existing practice bed
#779 opened Jul 26, 2024 by EricR86
5
FORMAT field CICN and its relation to CN field vcf
#778 opened Jul 18, 2024 by vasudeva8
@d-cameron
Number, type and description on FORMAT not in sync with List of changes vcf
#777 opened Jul 18, 2024 by vasudeva8
vcf: Invalid unstructured header line in VCF 4.3 example complexfile_passed_000.vcf vcf
#772 opened May 31, 2024 by zaeleus
1
@d-cameron
2
refget: v2 spec for Range header errors does not align with typical usage refget
#771 opened May 29, 2024 by davidlougheed
VCF4.4 SVLEN requirement across different variant representations vcf
#769 opened May 2, 2024 by tcezard
6
VCF Draft 4.5 and Modified Bases vcf
#767 opened Apr 22, 2024 by cjw85 VCFv4.5 RC1
@d-cameron
29
Questions about third-party use of test data
#766 opened Apr 19, 2024 by athos
6
CSI file is BGZF compressed but this is not mentioned in the CSV1 spec
#765 opened Apr 13, 2024 by bguo068
2
FAIRsharing Record Query - BED format bed
#746 opened Nov 15, 2023 by allysonlister
@michaelmhoffman
What does . mean for an A, R, or G indexed field? vcf
#737 opened Jul 31, 2023 by danking
@d-cameron
6
Consider 64-bit values in BCF, BAM and CRAM cram sam vcf
#735 opened Jul 18, 2023 by jkbonfield
2
Circular chromosomes in the VCF header vcf
#733 opened Jul 5, 2023 by nh13
1
sam-tags: MM field value pattern does not allow ambiguity codes sam sam-tags
#732 opened Jun 27, 2023 by zaeleus
3
ProTip! Find all open issues with in progress development work with linked:pr.