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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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[bcftools mpileup --samples-file] how to rename old sample names if they are not unique?
#2022
mlin2017
closed
10 months ago
3
bcftools norm: Reference allele mismatch if there are special characters preceding or following the reference description
#2021
pdagosto
closed
10 months ago
12
bcftools norm Segmentation fault (core dumped)
#2020
Rohit-Satyam
closed
11 months ago
3
pludgin "+fill-tags" doesn't work with deletions
#2019
carolynzy
closed
10 months ago
1
bcftools mpileup error: rcns_set_reads todo: unknown cigar operator 3
#2018
webbchen
closed
10 months ago
2
bcftools concat doesn't work !
#2017
jefflllyyy
closed
2 months ago
1
Bcftools annotate overwrite existing tag
#2016
valeandri
opened
11 months ago
2
[mpileup | call] Output ALT <NON_REF> or <*> instead of a dot into gVCF reference blocks
#2015
PlatonB
closed
10 months ago
4
MNV not being atomized by bcftools norm
#2014
gevro
closed
7 months ago
9
bcftools mpileup Illumina-1.3+ encoding
#2013
gangxuehzau
closed
11 months ago
1
Annotating vcfs with AFs for roh
#2012
kittysher
closed
7 months ago
8
Missing data format issue
#2011
jaurbanChicago
closed
11 months ago
1
Split-vep error with version 1.12 and 1.18
#2010
GACGAMA
closed
11 months ago
1
Duplicate sample error with reheader
#2009
sethsh7
closed
11 months ago
1
[Feature Request] Allow --write-index to choose tbi index output
#2008
rickymagner
closed
5 months ago
5
Option to move filter to format in merge
#2007
mbhall88
opened
11 months ago
1
[Feature Request] Index multiple files at once
#2006
rickymagner
closed
11 months ago
1
bcftools filter -e doesn't work for gVCF REF field
#2005
PlatonB
closed
11 months ago
1
Can you filter for private 1/1 genotype?
#2004
Axze-rgb
closed
11 months ago
1
Is this the kind of distribution expected for the BQBZ metrics?
#2003
Axze-rgb
closed
11 months ago
0
question: maintaining source information on bcftools concat
#2002
zeeev
closed
11 months ago
1
How does bcftools +contrast diverges from merging and using -x
#2001
Axze-rgb
closed
11 months ago
2
bcftools run over 18 hours only calling 11Mb sequence of one chromosome
#2000
leon945945
opened
12 months ago
19
bcftools does not appear to handle SIGPIPE gracefully
#1999
anderspitman
closed
11 months ago
2
bcftools annotate does not overwrite existing entries in header with -h flag
#1998
rickymagner
opened
1 year ago
2
Question about isec output
#1997
bioinfoMMS
closed
1 year ago
5
bcftools view problem
#1995
MattHegarty431
closed
1 year ago
2
Expanding dereplicated reads
#1996
tkchafin
opened
1 year ago
2
How to efficiently find complement between many vcf?
#1994
Axze-rgb
closed
1 year ago
1
potential improvement for summary line from bcftools norm
#1993
biorococo
closed
1 year ago
1
bcftools query; sample names missing in header line
#1992
WimSpee
closed
1 year ago
2
bcftools mpileup and call with large bam files
#1991
dosshra
closed
1 year ago
3
bcftools merge crash (develop branch)
#1990
jkbonfield
closed
1 year ago
2
bcftools annotate fail to mark sites by bed file
#1989
ruslan-abasov
closed
1 year ago
2
Print only samples with alternate (non-reference) genotypes
#1988
MaryamEO
closed
1 year ago
6
bcftools fill-tags custom INFO/TAG expression
#1987
AkkshayaRajesh
closed
1 year ago
1
urgent: error during consensus generation by applying variants
#1986
Cricetinae-hamster
closed
1 year ago
1
Invalid index is produced by --write-index and --threads
#1985
lacek
closed
12 months ago
0
bcftools isec to extract unique snps
#1983
Nikhilgunala
closed
1 year ago
2
Filtering indels
#1982
lt11
closed
1 year ago
3
Feature request: filter snps near other snps
#1981
gevro
closed
1 year ago
2
Fix grammar in bcftools gtcheck help
#1980
ghuls
closed
1 year ago
1
[E::vcf_parse_format] Invalid character 'i' in 'CN' FORMAT field at chrM:1
#1979
jingydz
closed
1 year ago
1
error while running bcftools to split vcf file
#1978
FrancisNietzsche
opened
1 year ago
1
Undocumented Behaviour of Annotate Module if INFO Tag Already Exists
#1977
DarioS
closed
1 year ago
1
bcftools: error while loading shared libraries: libcrypto.so.1.0.0: cannot open shared object file: No such file or directory
#1976
swajid
closed
1 year ago
2
fill-tags to compute values according to genotype
#1975
edg1983
opened
1 year ago
5
bcftools merge --info-rules - doesn't disable rules
#1974
audrey-bollas
opened
1 year ago
1
bcftools merge raises segmentation fault
#1972
alexeybondarev
closed
1 year ago
3
Understanding order of operations when filtering
#1971
reubwn
closed
1 year ago
1
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