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280 Open 1,583 Closed
280 Open 1,583 Closed
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Issues list

Problem with binomial calculation
#2186 opened May 17, 2024 by chundruv
bcftools mpileup + call seemingly confident in allele only present in a few reads?
#2185 opened May 17, 2024 by emos8710
1
bcftools mpileup handling of corrupted/truncated data/streaming errors
#2177 opened May 1, 2024 by kachulis
2
"bcftools norm -m -any" prdocues "." htslib-dependent Cannot be fixed until htslib is fixed
#2173 opened Apr 29, 2024 by shahamer
1
bcftools view -S data size vcf
#2170 opened Apr 25, 2024 by hitwbt
1
Could bcftools report all states of characters for very low coverage?
#2141 opened Mar 26, 2024 by Axze-rgb
4
bcftools reheader Incomplete File if Output Same as Input enhancement
#2140 opened Mar 26, 2024 by DarioS
1
bcftools norm -m +any gives incorrect AN value when SNP and INDEL entries are merged
#2137 opened Mar 24, 2024 by Fan-iX
Fix reference needs-feedback
#2125 opened Mar 15, 2024 by sonalipechlivanis
2
bcftools consensus --mark-ins
#2124 opened Mar 12, 2024 by loieeyet
2
Incorrect interpretation of fixed ALT homozygotes from bcftools filter? requires-test-case
#2123 opened Mar 8, 2024 by pmoizerv
1
problem changing the ploidy of female individuals on the sex chromosome requires-test-case
#2122 opened Mar 8, 2024 by TanguyMuller
3
Possible 4x speed up of merge --gvcf ref.fa
#2106 opened Feb 21, 2024 by pd3
1
Conversion from standard VCF to Local-alleles VCF
#2105 opened Feb 20, 2024 by jkbonfield
3
Updating filter syntax and threshold ? documentation enhancement
#2101 opened Feb 18, 2024 by davidyuyuan
1
Mention somewhere that multiallelic variants need to be expanded with bcftools norm --multiallelics +both if you want to remove overlaps with bcftools +remove-overlaps
#2085 opened Jan 24, 2024 by ghuls
Find polymorphic genotypes from merged vcf file
#2083 opened Jan 24, 2024 by bioinfoanalyst
1
Remove overlaps not working as expected
#2082 opened Jan 24, 2024 by mbhall88
6
Absolutly All positions in mpileup (previously -aa)
#2076 opened Jan 17, 2024 by jlapaijmans
5
Use REF, ALT, etc as regex in filter expressions
#2074 opened Jan 9, 2024 by njspix
bcftools-1.19 csq: output is not compatible with previous --local-csq format
#2073 opened Jan 9, 2024 by mmokrejs
1
bcftools mpileup call with empty output
#2069 opened Jan 5, 2024 by valentinaOpazo
5
Fail to subset VCF file by chromosomes requires-test-case
#2067 opened Jan 4, 2024 by MaayanYoles
3
merge command collapsing non-identical variants to single record needs-feedback
#2063 opened Dec 21, 2023 by Logan-Wallace
1
homozygous with equal allele depth requires-test-case
#2056 opened Dec 13, 2023 by abhortas
2
ProTip! Exclude everything labeled bug with -label:bug.