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312 Open 1,725 Closed
312 Open 1,725 Closed
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Issues list

bcftools annotate produces truncated vcf with exit code 0
#2385 opened Mar 21, 2025 by dennishendriksen
Regarding how bcftools +count distinguishes and identifies SNPs, INDELs, and MNPs.
#2384 opened Mar 18, 2025 by ZhaoTie-re
[Request] bcftools reheader -s should also be able to take a string as input
#2383 opened Mar 14, 2025 by famosab
bcftools mpileup memory use with single vs. multiline BED file
#2382 opened Mar 12, 2025 by marqueda
bcftools mpileup issue calling indels
#2381 opened Mar 12, 2025 by tdunham19
3
bcftools call Doesn't Seem to Understand Negated Sample Argument
#2380 opened Mar 12, 2025 by fbschmtt
mendelian2 plugin
#2379 opened Mar 11, 2025 by biouserPD
"-nan" GP and genotype coding in males
#2377 opened Mar 7, 2025 by rcheng
4
How to compute DS (diploid dosage) from HDS (haploid dosage) in VCF? needs-feedback
#2376 opened Mar 5, 2025 by NadiAlipour
1
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 (v4.2 Number=.)
#2371 opened Feb 27, 2025 by davmlaw
4
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
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