Skip to content

Issues: samtools/bcftools

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

308 Open 1,720 Closed
308 Open 1,720 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

How to compute DS (diploid dosage) from HDS (haploid dosage) in VCF?
#2376 opened Mar 5, 2025 by NadiAlipour
Question about BCFtools +prune: how does it shift the window through the reference genome?
#2373 opened Feb 28, 2025 by Hugh-Zhu
1
norm split multiallelics does not split SVLEN
#2371 opened Feb 27, 2025 by davmlaw
2
Alternative genetic codes in bcftools csq for mitochondrial variant annotation
#2368 opened Feb 24, 2025 by etwatson
2
Using COUNT with bcftools filter across all samples
#2363 opened Feb 1, 2025 by mhoban
2
bcftools 1.21 merge gvcfs results in more than one variant at the same location for complex polyallelic MNP variants, continuation of #2333
#2356 opened Jan 21, 2025 by jcm6t
The genotypes do not reflect the allele coverage frequency
#2352 opened Jan 9, 2025 by pailloufat-stack
Problems defining ploidy with bcftools call
#2351 opened Jan 7, 2025 by amankowski
1
2 lines of InDel in the same position ?
#2347 opened Dec 24, 2024 by Jerry-Wang-Dog
1
feature request: duplicate merging and selecting
#2342 opened Dec 18, 2024 by davmlaw
1
Merge speed has not been increased by '--threads' option ?
#2340 opened Dec 17, 2024 by Jerry-Wang-Dog
2
how to subset .vcf.gz file to include only variants whose genomic coordinates are given in a list requires-test-case
#2332 opened Dec 9, 2024 by annilk
8
strange handling of SVs by bcftools norm --fasta-ref requires-test-case
#2330 opened Dec 6, 2024 by maggs-x
3
Different parameters on different chromosomes needs-feedback
#2327 opened Dec 1, 2024 by JJ0ONATHANESTAR
1
[Feature Request] Cannot sort using custom contig order enhancement
#2324 opened Nov 26, 2024 by rickymagner
2
Filter a gene list including intergenic regions needs-feedback
#2319 opened Nov 12, 2024 by ccbruels
3
Consensus of ALTs only without genotypes in file enhancement
#2315 opened Nov 9, 2024 by schorlton-bugseq
2
seg fault for reheader -o requires-test-case
#2311 opened Oct 30, 2024 by Ahuiting
3
Error "Failed to read from standard input: unknown file type" with Gzipped BAM Files
#2293 opened Sep 27, 2024 by Silvia-lme
1
How to populate Fisher test annotation
#2287 opened Sep 26, 2024 by pd3
1
Document / Improve / Polish / Fix --indels-2.0 bug D1: Difficult enhancement P2: Desirable
#2280 opened Sep 17, 2024 by jkbonfield
3
Significant difference between IDV and AD when calling certain RNA-seq indels with mpileup
#2277 opened Sep 12, 2024 by luyh-xp
2
8
Variable expansion issue with +setGT? [$VARIABLE-] isn't working...
#2276 opened Sep 9, 2024 by goeckeritz
1
annotate add INFO/tag form CHROM-POS-REF-ALT
#2273 opened Sep 6, 2024 by user-tq
annotate ID for multi-allelic sites
#2264 opened Aug 20, 2024 by ikarus97
1
ProTip! Follow long discussions with comments:>50.