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313 Open 1,695 Closed
313 Open 1,695 Closed
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Issues list

plot-vcfstats -s leads to IndexError: list index out of range
#2353 opened Jan 9, 2025 by warthmann
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
consensus --missing not compatible with gvcf blocks
#2350 opened Jan 7, 2025 by Fan-iX
Bcftools query does not recognize arithmetic functions
#2349 opened Dec 31, 2024 by smlchen
Error occurred while processing INFO tag "RPA" when use bcftools merge
#2348 opened Dec 30, 2024 by TuBieJun
2 lines of InDel in the same position ?
#2347 opened Dec 24, 2024 by Jerry-Wang-Dog
mpileup's off-by-one bug: when cannot parse contig name with a comma, subsequent output is wrongly labeled
#2345 opened Dec 19, 2024 by azaznaev
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
recovering multiallelics with bcftools norm is changing reference alleles to missing
#2339 opened Dec 16, 2024 by bwspitzer
2
how to subset .vcf.gz file to include only variants whose genomic coordinates are given in a list
#2332 opened Dec 9, 2024 by annilk
5
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
How to Generate Haplotype 1 and 2 FASTA Files Using Phased VCF from HiPhase
#2310 opened Oct 24, 2024 by ClarenceHsiang
1
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
ProTip! no:milestone will show everything without a milestone.