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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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Missing decimal points in DP
#2075
tkn132
closed
6 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
Fail to subset VCF file by chromosomes
#2067
MaayanYoles
opened
6 months ago
3
[feature request] Option to use temporary files for `bcftools merge`
#2066
hjeremyli
closed
6 months ago
2
Feature request: --new-gt c:0/X
#2065
pd3
closed
6 months ago
0
gvcfz plugin is undocumented
#2064
PlatonB
closed
7 months ago
1
merge command collapsing non-identical variants to single record
#2063
Logan-Wallace
opened
7 months ago
1
Improve docs on --soft-filter argument.
#2062
SpikyClip
closed
7 months ago
1
bcftools: error while loading shared libraries: libcrypto.so.1.0.0: cannot open shared object file: No such file or directory (
#2061
PhyloGrok
closed
7 months ago
1
For help, an error in bcftools filter
#2060
H2023-L
closed
7 months ago
0
address multiple typos
#2059
emollier
closed
6 months ago
7
bcftools 1.19 - consensus - different warnings for overlapping variants
#2058
salvatoreloguercio
closed
6 months ago
1
bcftools +split-vep -s worst; Too few columns at chr1:69059 .. 1 (Consequence) >= 1
#2057
robertzeibich
closed
7 months ago
1
homozygous with equal allele depth
#2056
abhortas
opened
7 months ago
2
Incorrect number of FORMAT/GL values with bcftools tag2tag output
#2055
isinaltinkaya
closed
7 months ago
1
MAF Filtering - difference between two approaches
#2054
nirav572
closed
7 months ago
2
--ploidy 2 function not working?
#2053
officialnaturalist
closed
7 months ago
1
bcftools consensus genome, get not all chromosomes sequences!
#2052
CrawlingSponge
opened
7 months ago
1
Clarifying CSQ's ncsq
#2051
barneyhill
closed
7 months ago
1
bcftools norm don't move some variants to the far left.
#2050
tanger-code
closed
7 months ago
1
Documentation for the output of bcftools stats dosage r-squared
#2049
YuqinGu-bio
opened
7 months ago
0
Combining --merge options in bcftools merge ?
#2048
yvanw
opened
7 months ago
0
bcftools sort has duplicate -O in the usage
#2047
nh13
closed
7 months ago
1
Check fclose(stdout) at the end of main() [and miscellanea]
#2046
jmarshall
opened
8 months ago
0
revision of 1679 plus switch to edlib over BAQ
#2045
jkbonfield
closed
5 months ago
32
Portability improvements
#2044
daviesrob
closed
6 months ago
0
Fix bus error in bcftools merge on armhf (32-bit hard-float)
#2042
daviesrob
closed
8 months ago
1
ROH `--rec-rate` Default?
#2041
christopherdkoch
opened
8 months ago
0
make USE_GPL=1 clean all fails because GSL_LIBS already defined
#2040
tobiasrausch
closed
6 months ago
3
+split-vep --include not able to properly filter float columns extracted from CSQ
#2039
SpikyClip
closed
7 months ago
1
`bcftools sort` assertion failed
#2043
meganbg
opened
8 months ago
1
bcftools 1.19 annotate not working with "." and "+" modifiers for adding TAG fields
#2038
epsalazarf
closed
8 months ago
1
Issue with Reference Allele Mismatch in bcftools norm,Reference allele mismatch ...
#2037
karen916
closed
8 months ago
1
test_vcf_merge failures on arm 32-bit with FPU: Bus error
#2036
emollier
closed
8 months ago
12
indel ALT gets removed during calling, but leaves invalid indel line
#2035
mcolpus
closed
8 months ago
1
`bcftools filter --exlude FILTER~"multiallelic"` causes `No such INFO field: multiallelic`
#2034
monagai
closed
8 months ago
3
filter for format field using ALT column
#2033
arpanda
opened
8 months ago
1
skip sites if one sample in the pair is missing data?
#2032
goeckeritz
closed
8 months ago
6
bcftools mpileup: interpreting AD (Allelic depth) annotation
#2031
rmurray2
closed
8 months ago
1
bcftools call changing ploidy option gives very different results
#2030
rmurray2
closed
8 months ago
1
bcftools norm <DEL> for very long variants
#2029
christopher-schroeder
closed
8 months ago
1
--regions/--targets does not return overlapping insertion when overlap is set to (1|2)
#2028
bryce-turner
closed
9 months ago
3
If I put two adjacent small variants together, will it be divided into two variants by "bcftools norm"?
#2027
tanger-code
closed
8 months ago
1
Quick Question - Bcftools Consensus for Indels
#2026
NicMAlexandre
opened
9 months ago
1
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