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samtools
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bcftools
This is the official development repository for BCFtools. See installation instructions and other documentation here http://samtools.github.io/bcftools/howtos/install.html
http://samtools.github.io/bcftools/
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Don't change indel qual when indelQ == 0.
#2121
jkbonfield
closed
3 months ago
1
Observations on multi-samp calling
#2120
jkbonfield
closed
4 months ago
2
Help separating alleles for 'merge' when ploidy >2
#2119
IsaacTollestrup
closed
2 months ago
1
bcftools call segfaulting when using a -Aim -C alleles -T
#2118
sahwa
closed
4 months ago
0
mpileup --indels-cns and varying indel sizes
#2117
jkbonfield
closed
3 months ago
1
bedtools multicov is returing Could not find/load indexes
#2116
NiharikaCUSB
closed
3 months ago
1
[mpileup] 1 samples in 12 input files
#2115
xiadawei123
closed
3 months ago
1
bcftools norm not working as expected for Number=G fields
#2114
SteampunkIslande
closed
3 months ago
1
Apparent de novo deletion is not recognized as such with --indels-cns
#2113
pd3
closed
3 months ago
8
How can bcftools filter samples with large fraction of missing site?
#2112
Neo-xbx-00
closed
3 months ago
1
Segmentation fault on `INFO/TAG=@file.txt` if TAG does not exist in first record
#2111
bryce-turner
closed
3 months ago
1
fail to call indels using command "bcftools call"
#2110
Amatatsu15
closed
4 months ago
2
Why some alleles were missed in genotypes even they have AD values.
#2109
idadoudou
closed
3 months ago
2
Fix a trivial memory leak in the mpileup usage (etc) code
#2108
jkbonfield
closed
4 months ago
0
Computation of INFO tags in bcftools +fill-tags
#2107
nirav572
closed
3 months ago
2
Possible 4x speed up of merge --gvcf ref.fa
#2106
pd3
opened
4 months ago
1
Conversion from standard VCF to Local-alleles VCF
#2105
jkbonfield
opened
4 months ago
3
bcftools split vep miss variant without allele frequency when using -f to print gnom_af
#2104
liuhankui
closed
4 months ago
2
bcftools sort problem?
#2103
SZ-qing
closed
4 months ago
3
memory issue when sum(AD) > DP in bcftools stats -s
#2102
23andme-jaredo
closed
4 months ago
4
Updating filter syntax and threshold ?
#2101
davidyuyuan
opened
4 months ago
1
bcftools merge: support single-file edge case [enhancement]
#2100
jan-glx
closed
4 months ago
1
`bcftools concat --write-index` does not produce an index
#2099
blaiseli
closed
4 months ago
1
Can't filter custom VEP annotations which are float numbers
#2098
GACGAMA
closed
4 months ago
1
beftools merging 3540 individual files
#2097
Biophylo2001
closed
4 months ago
3
Inverse consensus VCF
#2096
mbhall88
closed
4 months ago
4
bcftools call: Segmentation fault. vcfcall.c:597 ` if ( als[1][0]=='<' ) return 0;`
#2095
lindenb
closed
4 months ago
1
"bcftools csq" introducing reference-based bias
#2094
mmokrejs
closed
4 months ago
1
Settings to reduce reference bias?
#2093
elsemikk
closed
4 months ago
1
bcftools isec support for a --file-list?
#2092
jhampstead
closed
4 months ago
1
bcftools consensus with deletions starting outside region of interest
#2091
nage0178
closed
4 months ago
3
bcftools norm (join biallelics) turns phased into unphased GTs
#2090
tobiasrausch
closed
5 months ago
2
bcftools reheader to support stdin?
#2088
clintval
closed
3 months ago
2
[E::bcf_get_variant_type] Requested allele outside valid range
#2086
MartaAlberti
closed
5 months ago
2
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
ghuls
opened
5 months ago
0
`bcftools norm --multiallelics -indels` does not normalize indels.
#2084
ghuls
closed
5 months ago
2
Find polymorphic genotypes from merged vcf file
#2083
bioinfoanalyst
opened
5 months ago
1
Remove overlaps not working as expected
#2082
mbhall88
opened
5 months ago
6
Suggested function: bcftools consensus region
#2080
kfpbennett
closed
5 months ago
2
split-vep incorrectly outputs cDNA, CDS and protein positions
#2079
bartcharbon
closed
5 months ago
3
Update copyright date in LICENSE file and version messages
#2077
daviesrob
closed
5 months ago
0
Absolutly All positions in mpileup (previously -aa)
#2076
jlapaijmans
opened
5 months ago
5
Missing decimal points in DP
#2075
tkn132
closed
5 months ago
6
Use REF, ALT, etc as regex in filter expressions
#2074
njspix
opened
6 months ago
0
bcftools-1.19 csq: output is not compatible with previous --local-csq format
#2073
mmokrejs
opened
6 months ago
1
bcftools-1.19: core dump in init_data() at plugins/split-vep.c:602
#2072
mmokrejs
closed
6 months ago
3
transcript select for mane and pick in split-vep
#2071
barslmn
closed
6 months ago
7
bcftools-1.19 csq does not add FORMAT/BCSQ to all lines
#2070
mmokrejs
closed
6 months ago
4
bcftools mpileup call with empty output
#2069
valentinaOpazo
opened
6 months ago
6
bcftools-1.19 csq: generates BCSQ but some tools anticipate CSQ instead
#2068
mmokrejs
closed
6 months ago
4
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