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316 Open 1,685 Closed
316 Open 1,685 Closed
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Issues list

Feature request: norm --remove-duplicates report removed dupes in summary stats
#2346 opened Dec 20, 2024 by davmlaw
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
bcftools stats does not return any information on the complements
#2344 opened Dec 19, 2024 by laura-an
1 bp insertion supported by deep sequencing missed by bcftools mpile/call
#2343 opened Dec 19, 2024 by carolynzy
feature request: duplicate merging and selecting
#2342 opened Dec 18, 2024 by davmlaw
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
fill-tags VAF and VAF1 not working for multi-allelic sites
#2338 opened Dec 16, 2024 by bartcharbon
bcftools query: referencing ID column when there is a META field named ID?
#2337 opened Dec 13, 2024 by bbimber
bcftools norm: Why did it "normalize" this deletion by shifting REF 5' by 29 bp?
#2336 opened Dec 13, 2024 by toddajohnson
1
bcftools annotate labels transferred FILTER column as single value "Number=1" in header
#2335 opened Dec 13, 2024 by toddajohnson
bcftools 1.20 merge gvcfs results in more than one variant at the same location for complex polyallelic MNP variants requires-test-case
#2333 opened Dec 9, 2024 by jcm6t
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
3
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
Problem with specifying filtering expression v1.21
#2322 opened Nov 20, 2024 by reshu23
6
Filter a gene list including intergenic regions
#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
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