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This is the official development repository for BCFtools. To compile, the develop branch of htslib is needed: git clone --branch=develop git://github.com/samtools/htslib.git htslib

samtools.github.io/bcftools/

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2,323 Commits
.travis
.travis
 
 
doc
doc
 
 
m4
m4
 
 
misc
misc
 
 
plugins
plugins
 
 
test
test
 
 
.appveyor.yml
.appveyor.yml
 
 
.cirrus.yml
.cirrus.yml
 
 
.gitattributes
.gitattributes
 
 
.gitignore
.gitignore
 
 
.travis.yml
.travis.yml
 
 
AUTHORS
AUTHORS
 
 
HMM.c
HMM.c
 
 
HMM.h
HMM.h
 
 
INSTALL
INSTALL
 
 
LICENSE
LICENSE
 
 
Makefile
Makefile
 
 
NEWS
NEWS
 
 
README
README
 
 
README.md
README.md
 
 
bam2bcf.c
bam2bcf.c
 
 
bam2bcf.h
bam2bcf.h
 
 
bam2bcf_indel.c
bam2bcf_indel.c
 
 
bam_sample.c
bam_sample.c
 
 
bam_sample.h
bam_sample.h
 
 
bcftools.h
bcftools.h
 
 
bin.c
bin.c
 
 
bin.h
bin.h
 
 
call.h
call.h
 
 
ccall.c
ccall.c
 
 
cols.c
cols.c
 
 
cols.h
cols.h
 
 
config.mk.in
config.mk.in
 
 
configure.ac
configure.ac
 
 
consensus.c
consensus.c
 
 
convert.c
convert.c
 
 
convert.h
convert.h
 
 
csq.c
csq.c
 
 
dist.c
dist.c
 
 
dist.h
dist.h
 
 
em.c
em.c
 
 
extsort.c
extsort.c
 
 
extsort.h
extsort.h
 
 
filter.c
filter.c
 
 
filter.h
filter.h
 
 
gvcf.c
gvcf.c
 
 
gvcf.h
gvcf.h
 
 
hclust.c
hclust.c
 
 
hclust.h
hclust.h
 
 
hex.h
hex.h
 
 
install-sh
install-sh
 
 
khash_str2str.h
khash_str2str.h
 
 
kheap.h
kheap.h
 
 
kmin.c
kmin.c
 
 
kmin.h
kmin.h
 
 
main.c
main.c
 
 
mcall.c
mcall.c
 
 
mpileup.c
mpileup.c
 
 
mw.h
mw.h
 
 
peakfit.c
peakfit.c
 
 
peakfit.h
peakfit.h
 
 
ploidy.c
ploidy.c
 
 
ploidy.h
ploidy.h
 
 
polysomy.c
polysomy.c
 
 
prob1.c
prob1.c
 
 
prob1.h
prob1.h
 
 
rbuf.h
rbuf.h
 
 
regidx.c
regidx.c
 
 
regidx.h
regidx.h
 
 
reheader.c
reheader.c
 
 
smpl_ilist.c
smpl_ilist.c
 
 
smpl_ilist.h
smpl_ilist.h
 
 
tabix.c
tabix.c
 
 
tsv2vcf.c
tsv2vcf.c
 
 
tsv2vcf.h
tsv2vcf.h
 
 
variantkey.h
variantkey.h
 
 
vcfannotate.c
vcfannotate.c
 
 
vcfbuf.c
vcfbuf.c
 
 
vcfbuf.h
vcfbuf.h
 
 
vcfcall.c
vcfcall.c
 
 
vcfcnv.c
vcfcnv.c
 
 
vcfconcat.c
vcfconcat.c
 
 
vcfconvert.c
vcfconvert.c
 
 
vcffilter.c
vcffilter.c
 
 
vcfgtcheck.c
vcfgtcheck.c
 
 
vcfindex.c
vcfindex.c
 
 
vcfisec.c
vcfisec.c
 
 
vcfmerge.c
vcfmerge.c
 
 
vcfnorm.c
vcfnorm.c
 
 
vcfplugin.c
vcfplugin.c
 
 
vcfquery.c
vcfquery.c
 
 
vcfroh.c
vcfroh.c
 
 
vcfsom.c
vcfsom.c
 
 
vcfsort.c
vcfsort.c
 
 
vcfstats.c
vcfstats.c
 
 
vcfview.c
vcfview.c
 
 
vcmp.c
vcmp.c
 
 
vcmp.h
vcmp.h
 
 
version.c
version.c
 
 
version.sh
version.sh
 
 

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Build Status

This is the official development repository for BCFtools. It contains all the vcf* commands which previously lived in the htslib repository (such as vcfcheck, vcfmerge, vcfisec, etc.) and the samtools BCF calling from bcftools subdirectory of samtools.

For a full documentation, see bcftools GitHub page.

Other useful links:

File format specifications live on HTS-spec GitHub page htslib samtools tabix

About

This is the official development repository for BCFtools. To compile, the develop branch of htslib is needed: git clone --branch=develop git://github.com/samtools/htslib.git htslib

samtools.github.io/bcftools/

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