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
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.travis Travis builds clone corresponding htslib branch Feb 19, 2015
doc Expand docs as suggested by #654 Nov 17, 2018
m4 Add configure options to enable warnings and optionally Werror. See a… May 16, 2018
misc Division in Python3 is floating point by default, make plot-vcfstats … Aug 21, 2018
plugins New -a, --alt-trios option to +trio-stats Nov 11, 2018
test Output records from `call -i -C allele -T tab` in the correct order. F… Nov 19, 2018
.gitattributes Travis builds clone corresponding htslib branch Feb 19, 2015
.gitignore Update variantkey with the new header-only version Sep 6, 2018
.travis.yml Add --enable-libgsl option to autoconf Jun 9, 2017
AUTHORS Added missing contributors Feb 4, 2015
HMM.c Fix HMM initilization in ROH when snapshots are used in multiple chro… May 10, 2017
HMM.h Fix HMM initilization in ROH when snapshots are used in multiple chro… May 10, 2017
INSTALL Add package install suggestions to INSTALL Jul 12, 2018
LICENSE Add license title Jul 19, 2018
Makefile Update variantkey with the new header-only version Sep 6, 2018
NEWS New reheader -f,--fai option. Resolves #860 Aug 24, 2018
README Add basic INSTALL and README files Aug 15, 2014
README.md stats: Updated to work with modified htslib/bcf_regions; More tests f… Dec 5, 2013
bam2bcf.c Fix mpileup's incorrect FMT/AD indel depths Jun 11, 2017
bam2bcf.h mpileup: support multiple regions Aug 5, 2016
bam2bcf_indel.c Fix mpileup's incorrect FMT/AD indel depths Jun 11, 2017
bam_sample.c Fix warnings identified with -fsanitize=address Jul 17, 2018
bam_sample.h mpileup: include reads with unlisted or missing RG ID to match previo… Aug 5, 2016
bcftools.h Clean error reporting code and warn if incorrect parameters given. Re… May 23, 2018
bin.c Finally fix #801 Jul 18, 2018
bin.h stats: make the AF binning code reusable Aug 2, 2016
call.h `call -C allels -i` should not skip sites. Fixes #913 Nov 17, 2018
ccall.c Fix #599 Apr 28, 2017
config.mk.in Support for custom -i/-e perl script filtering Mar 15, 2018
configure.ac Do not change license to GPL with ./configure --enable-perl-filters Jul 3, 2018
consensus.c Make consensus work with insertions immediately following deletions Oct 3, 2018
convert.c Add phred() to filtering expressions and %PBINOM to query Nov 12, 2018
convert.h Make query output only matching genotype fields Nov 12, 2017
csq.c Fix in csq for embedded transcripts Nov 19, 2018
em.c Canonicalise whitespace -- USE -b/-w TO DIFF/BLAME ACROSS THIS COMMIT Aug 14, 2014
filter.c Remove nonsense code; make binom and phred work on different platforms Nov 13, 2018
filter.h Speedup of `bcftools query` when FORMAT fields are not printed Jun 12, 2015
gvcf.c Check return status of all *write() and *close() calls Jul 19, 2018
gvcf.h Bringing "call --gvcf" from experimental to main repo. Sep 30, 2015
hclust.c gtcheck: prevent segfault with positive values of `-c max` Aug 3, 2016
hclust.h gtcheck: improved cross-check mode Aug 3, 2016
hex.h Update variantkey with the new header-only version Sep 6, 2018
install-sh bring over autoconf etc files from samtools unchanged Jun 9, 2017
khash_str2str.h reheader: support spaces in sample names Jan 14, 2016
kheap.h New sort command Jul 6, 2017
kmin.c call: Original bcftools' -c calling now functional Oct 1, 2013
kmin.h call: Original bcftools' -c calling now functional Oct 1, 2013
main.c Update copyright date printed by bcftools --version Jul 13, 2018
mcall.c More informative error message to help resolve issues like #915 Nov 17, 2018
mpileup.c IDV and IMF report raw indel reads before realignment, put this in th… Nov 13, 2018
mw.h Added copyright/license boilerplate to mw.h. Sep 15, 2016
peakfit.c peakfit build with GSLv2, resolves #378 Feb 12, 2016
peakfit.h update copyright dates for peakfit Jul 6, 2015
ploidy.c New bcftools/csq command, regidx overhaul and new %TBCSQ query format. Sep 2, 2016
ploidy.h regidx: import regidx api from htslib into bcftools Aug 5, 2016
polysomy.c Check return status of all *write() and *close() calls Jul 19, 2018
prob1.c Fix #599 Apr 28, 2017
prob1.h Fix #599 Apr 28, 2017
rbuf.h New +prune plugin May 17, 2017
regidx.c Fix a bug in regidx Jul 26, 2018
regidx.h Minor documentation update Jul 26, 2018
reheader.c Silence warnings [minor] Sep 13, 2018
smpl_ilist.c Make the sample mapping work again with `annotate`. Fixes #123 Sep 18, 2018
smpl_ilist.h Make the sample mapping work again with `annotate`. Fixes #123 Sep 18, 2018
tabix.c Tidy upsfor C99 / _XOPEN_SOURCE=700 compliance. Apr 5, 2017
tsv2vcf.c Tidy upsfor C99 / _XOPEN_SOURCE=700 compliance. Apr 5, 2017
tsv2vcf.h convert: New --gensample2vcf option; change in --gensample output, Sep 20, 2014
variantkey.h Update variantkey with the new header-only version Sep 6, 2018
vcfannotate.c Make the sample mapping work again with `annotate`. Fixes #123 Sep 18, 2018
vcfbuf.c Add new buffering functionality by overlap to vcfbuf Jun 12, 2017
vcfbuf.h Add new buffering functionality by overlap to vcfbuf Jun 12, 2017
vcfcall.c Output records from `call -i -C allele -T tab` in the correct order. F… Nov 19, 2018
vcfcnv.c Minor fix: add missing test file; add missing long options. Fixes #890 Sep 24, 2018
vcfconcat.c Check return status of all *write() and *close() calls Jul 19, 2018
vcfconvert.c Check return status of all *write() and *close() calls Jul 19, 2018
vcffilter.c Make the --IndelGap option decide which indel to keep based on QUAL, … Nov 13, 2018
vcfgtcheck.c Check return status of all *write() and *close() calls Jul 19, 2018
vcfindex.c Check return status of all *write() and *close() calls Jul 19, 2018
vcfisec.c Check return status of all *write() and *close() calls Jul 19, 2018
vcfmerge.c Add support for merging FORMAT strings, only Number=G tags not suppor… Jul 23, 2018
vcfnorm.c Fix a bug in duplicates removal. Oct 8, 2018
vcfplugin.c Check return status of all *write() and *close() calls Jul 19, 2018
vcfquery.c Give a meaningful error message when -f is not given to query. Resolves Aug 14, 2018
vcfroh.c Use utility function to clamp lookup table index Jul 18, 2018
vcfsom.c Silence warnings and fix error messages Jul 4, 2018
vcfsort.c sort: Allow mkdtemp() with custom -T directory, if it ends with XXXXXX. Nov 2, 2018
vcfstats.c Clean error reporting code and warn if incorrect parameters given. Re… May 23, 2018
vcfview.c Check return status of all *write() and *close() calls Jul 19, 2018
vcmp.c Correctly transfer Number=G annotations, Mar 15, 2018
vcmp.h Correctly transfer Number=G annotations, Mar 15, 2018
version.c Moved hts_bcf_wmode to be accesible by plugins Jul 28, 2015
version.sh Release 1.9 Jul 18, 2018

README.md

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