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314 Open 1,736 Closed
314 Open 1,736 Closed
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Issues list

bcftools consensus -S not subsetting samples
#2398 opened Apr 30, 2025 by RebekahMohn
could not parse the input VCF
#2397 opened Apr 29, 2025 by BrendaLee1
2
Print a warning if -r/R/-t/-T sequences use different chr naming convention than the VCF header
#2396 opened Apr 20, 2025 by pd3
Bcftools merge and concat need to check header versions and use the highest. htslib-dependent Cannot be fixed until htslib is fixed
#2395 opened Apr 17, 2025 by jkbonfield
1
bcftools norm convert non-ATGCN IUPAC to N however mpileup and call does not. requires-test-case
#2393 opened Apr 15, 2025 by gokalpcelik
3
norm normalizing reference ALT is not counted in stats or old-rec-tag
#2391 opened Apr 10, 2025 by davmlaw
concordance with indels issue needs-feedback
#2388 opened Mar 27, 2025 by jokelley
1
[Request] bcftools reheader -s should also be able to take a string as input
#2383 opened Mar 14, 2025 by famosab
bcftools call Doesn't Seem to Understand Negated Sample Argument requires-test-case
#2380 opened Mar 12, 2025 by fbschmtt
3
mendelian2 plugin requires-test-case
#2379 opened Mar 11, 2025 by biouserPD
1
"-nan" GP and genotype coding in males requires-test-case
#2377 opened Mar 7, 2025 by rcheng
6
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
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
consensus --missing not compatible with gvcf blocks
#2350 opened Jan 7, 2025 by Fan-iX
4
2 lines of InDel in the same position ?
#2347 opened Dec 24, 2024 by Jerry-Wang-Dog
2
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
11
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
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