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

samtools.github.io/bcftools/

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792 Commits
plugins
plugins
 
 
test
test
 
 
.gitignore
.gitignore
 
 
.travis.yml
.travis.yml
 
 
AUTHORS
AUTHORS
 
 
COPYING
COPYING
 
 
Makefile
Makefile
 
 
README.md
README.md
 
 
bcfidx.unused.c
bcfidx.unused.c
 
 
bcftools.1
bcftools.1
 
 
bcftools.h
bcftools.h
 
 
bcftools.txt
bcftools.txt
 
 
call.h
call.h
 
 
ccall.c
ccall.c
 
 
config.c
config.c
 
 
config.h
config.h
 
 
em.c
em.c
 
 
filter.c
filter.c
 
 
filter.h
filter.h
 
 
kmin.c
kmin.c
 
 
kmin.h
kmin.h
 
 
main.c
main.c
 
 
mcall.c
mcall.c
 
 
plot-vcfstats
plot-vcfstats
 
 
prob1.c
prob1.c
 
 
prob1.h
prob1.h
 
 
rbuf.h
rbuf.h
 
 
tabix.c
tabix.c
 
 
vcfannotate.c
vcfannotate.c
 
 
vcfcall.c
vcfcall.c
 
 
vcfconcat.c
vcfconcat.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
 
 
vcfquery.c
vcfquery.c
 
 
vcfroh.c
vcfroh.c
 
 
vcfsom.c
vcfsom.c
 
 
vcfstats.c
vcfstats.c
 
 
vcfutils.pl
vcfutils.pl
 
 
vcfview.c
vcfview.c
 
 
vcfview.unused.c
vcfview.unused.c
 
 
vcmp.c
vcmp.c
 
 
vcmp.h
vcmp.h
 
 
version.c
version.c
 
 

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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 bcftools+calling branch of htslib is needed: git clone --branch=bcftools+calling git://github.com/samtools/htslib.git htslib

samtools.github.io/bcftools/

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