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

306 Open 1,673 Closed
306 Open 1,673 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

bcftools csq Error: the fasta reference does not match the VCF REF allele at h2tg000007l:1000944
#2323 opened Nov 24, 2024 by leon945945
Problem with specifying filtering expression v1.21
#2322 opened Nov 20, 2024 by reshu23
Majority of SNPs have allele frequency = 0.000000
#2321 opened Nov 19, 2024 by ryanskiba
bcftools view -m 2 -M 2 referencePanel.vcf.gz（SV and SNP）
#2320 opened Nov 18, 2024 by SunWinner01
2
Filter a gene list including intergenic regions
#2319 opened Nov 12, 2024 by ccbruels
2
bcftools consensous fails to write to GCP
#2316 opened Nov 11, 2024 by Ieremie
Consensus of ALTs only without genotypes in file enhancement
#2315 opened Nov 9, 2024 by schorlton-bugseq
2
Error: bcftools csq --- splice_build_hap: Assertion `splice->tr->beg <= rbeg' failed.
#2313 opened Nov 7, 2024 by sbgonenc
seg fault for reheader -o
#2311 opened Oct 30, 2024 by Ahuiting
3
How to Generate Haplotype 1 and 2 FASTA Files Using Phased VCF from HiPhase
#2310 opened Oct 24, 2024 by ClarenceHsiang
1
Bcftools view——locate problematic genotype in GT field
#2309 opened Oct 24, 2024 by Lloyd-LiuSiyi
6
bcftools annotate - tag ID not defined
#2302 opened Oct 15, 2024 by ValentinaPeona
3
Issue with bcftools annotate
#2297 opened Sep 30, 2024 by HVHunt
1
bcftools csq: Change chromosome name requirement.
#2294 opened Sep 28, 2024 by niederhuth
1
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
Remove the * ALT Allele Reporting From a g.vcf Before (or After) Genotyping
#2258 opened Aug 14, 2024 by jon4thin
1
bcftools mpileup resulting in downstream unparsable vcf record with allele M needs-feedback
#2256 opened Aug 13, 2024 by anscholes
1
bcftools concat retry mechanisms? htslib-dependent Cannot be fixed until htslib is fixed
#2245 opened Aug 6, 2024 by graphenn
2
Bcftools mpileup needs-feedback
#2237 opened Jul 26, 2024 by Mashindersingh
1
ProTip! Mix and match filters to narrow down what you’re looking for.