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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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Erroneous ROH output
#2169
snakesch
closed
2 months ago
1
Read depth and allele depth is low / zero
#2168
irbinveliz
closed
2 months ago
1
Inconsistent number of SNPs from bcftools stats and plot-vcfstats
#2167
YifanWei1115
closed
2 months ago
1
Genotype Probability (GP) option for the dosage plugin
#2166
PaulTimmers
closed
2 months ago
1
The REF prefixes differ: G vs C (1,1) Failed to merge alleles at...., combining ddRAD and WGR
#2165
AliBasuony2022
closed
1 month ago
2
FeatureRequest: filling in INFO/QD and INFO/FS attributes
#2164
WimSpee
closed
2 months ago
3
bcftools merge assumed reference for INDELs
#2163
BinglanLi
closed
2 months ago
1
combining vcfs
#2162
javierAPC
closed
2 months ago
1
atomize option does not appear in bcftools-1.20 norm
#2161
calix015
closed
2 months ago
0
bcftools norm with --multi-overlaps . outputs different variants depending on allele order in the input variant
#2160
astaric
closed
2 months ago
1
[W::bcf_calc_ac] Incorrect number of AC fields at Chrxx:xxxxx. (This message is printed only once.)
#2159
leeleeleeaaaaaaaaaalee
closed
2 months ago
1
Incorrect bit field sizes in gff.h
#2158
jkbonfield
closed
2 months ago
1
Setting variant ID as the Nth record
#2157
ASLeonard
closed
2 months ago
2
bcftools mpileup for variant calling from nanopore long read sequences
#2156
emilydolivo97
closed
2 months ago
1
Issue in variant decomposition
#2155
46paillettes
closed
2 months ago
1
High quality reads determined?
#2154
jalalsiddiqui
closed
2 months ago
1
Minor bug with `index -m 0`.
#2153
jkbonfield
closed
2 months ago
1
Feature request: Turn off header numbers when using -H
#2152
ejgardner-insmed
closed
2 months ago
1
Feature Request: Allow for matching on INFO fields using annotate
#2151
ejgardner-insmed
closed
2 months ago
1
ref alt
#2150
C-YONG
closed
2 months ago
0
about the bcftools mpileup setting
#2148
cnxiaobo94
closed
1 month ago
1
the question about bcftools view
#2147
jingydz
closed
1 month ago
1
Bcftools view include based on multiple filters
#2146
SophieS9
closed
3 months ago
6
norm doesn't normalize <DUP> symbolic variants
#2145
davmlaw
closed
2 months ago
1
bcftools merge memory map error
#2144
MarcElosua
closed
3 months ago
4
Bcftools norm prints only the header
#2143
alexvasilikop
closed
2 months ago
3
Difference between --atom-overlaps and --multi-overlaps
#2142
alexvasilikop
closed
2 months ago
4
Could bcftools report all states of characters for very low coverage?
#2141
Axze-rgb
opened
3 months ago
4
bcftools reheader Incomplete File if Output Same as Input
#2140
DarioS
opened
3 months ago
1
Short option for write-index
#2139
mbhall88
closed
3 months ago
4
Remove -specs=...redhat-hardened... from Perl options
#2138
jmarshall
closed
3 months ago
1
`bcftools norm -m +any` gives incorrect `AN` value when SNP and INDEL entries are merged
#2137
Fan-iX
opened
3 months ago
0
Make --write-index=tbi work.
#2136
jkbonfield
closed
3 months ago
5
Add mpileup_bench/run_multi.sh for multi-sample evaluations
#2135
jkbonfield
closed
2 months ago
1
DIfference between "Absent", "Missing" and "Deletion" in bcftool consensus
#2134
Nagaemory
closed
3 months ago
1
Question on subscripting arrays of Number=R tags by alleles found in FORMAT/GT
#2133
acorvelo
closed
3 months ago
1
Fix REF indel calls for multi-sample calling.
#2132
jkbonfield
closed
3 months ago
2
Latest --indel-cns code fails to call hom-ref genotypes when one sample has an insertion
#2130
pd3
closed
3 months ago
1
Allow bcftools reheader --fai to read its input file from a stream
#2129
daviesrob
closed
3 months ago
1
How to filter on "NOVELAL" after using contrast
#2128
Axze-rgb
closed
3 months ago
3
can't add the VAF tag
#2127
boutrys
closed
3 months ago
2
Filtering using file.txt for specific fields
#2126
GACGAMA
closed
3 months ago
1
Fix reference
#2125
sonalipechlivanis
opened
3 months ago
2
bcftools consensus --mark-ins
#2124
loieeyet
opened
3 months ago
2
Incorrect interpretation of fixed ALT homozygotes from bcftools filter?
#2123
pmoizerv
opened
3 months ago
1
problem changing the ploidy of female individuals on the sex chromosome
#2122
TanguyMuller
opened
3 months ago
3
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
1 month ago
1
bcftools call segfaulting when using a -Aim -C alleles -T
#2118
sahwa
closed
4 months ago
0
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