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309 Open 1,714 Closed
309 Open 1,714 Closed
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Issues list

Unexpected behaviour of per-sample function on FORMAT tags
#2369 opened Feb 25, 2025 by joshuamschmidt
1
Alternative genetic codes in bcftools csq for mitochondrial variant annotation
#2368 opened Feb 24, 2025 by etwatson
Tune roh for highly homozygous (H < 1%) organisms?
#2365 opened Feb 13, 2025 by taprs
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
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
Remove the * ALT Allele Reporting From a g.vcf Before (or After) Genotyping
#2258 opened Aug 14, 2024 by jon4thin
1
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