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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
Branch: develop
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Latest commit f1f261b Jul 18, 2019
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.travis Travis builds clone corresponding htslib branch Feb 19, 2015
doc Make `annotate -l` also for records outside annotation intervals Jul 6, 2019
m4 Add configure options to enable warnings and optionally Werror. See a… May 16, 2018
misc Check if there is data available for the indel VAF plot. Fixes #1035 Jun 3, 2019
plugins Add +ad-bias --variant-type and support for multiallelic sites Jun 24, 2019
test Continuation of 2299ab6 Jul 15, 2019
.appveyor.yml Fix some test paths. Apr 15, 2019
.gitattributes Travis builds clone corresponding htslib branch Feb 19, 2015
.gitignore Build plugins as DLLs. Apr 15, 2019
.travis.yml Add address sanitizer check to travis May 30, 2019
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
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 Windows/Mingw/MSYS support. Apr 15, 2019
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 Fix warnings due to function attributes added in htslib Jan 21, 2019
bin.c Finally fix #801 Jul 18, 2018
bin.h stats: make the AF binning code reusable Aug 2, 2016
call.h Add new `bcftools call -G, --group-samples` option May 6, 2019
ccall.c Fix #599 Apr 28, 2017
cols.c Proof of principle implementation of the split-vep plugin. Mar 25, 2019
cols.h Proof of principle implementation of the split-vep plugin. Mar 25, 2019
config.mk.in Build plugins as DLLs. Apr 15, 2019
configure.ac Build plugins as DLLs. Apr 15, 2019
consensus.c Add new `-H 1pIu/2pIu` feature to consensus. Resolves #1027 Jun 6, 2019
convert.c Fix in `bcftools query -f'%END\n'` expressions Jun 26, 2019
convert.h Make query output only matching genotype fields Nov 12, 2017
csq.c Explain what TCE (encountered in GRCh38 gff3) means Jun 28, 2019
em.c Canonicalise whitespace -- USE -b/-w TO DIFF/BLAME ACROSS THIS COMMIT Aug 14, 2014
filter.c Merge pull request #609 from jkbonfield/jkb_win Jun 6, 2019
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 Build complete without plugins. Apr 15, 2019
mcall.c Fix possible out of bounds write in mcall_constrain_alleles() May 30, 2019
mpileup.c Add new `bcftools call -G, --group-samples` option May 6, 2019
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 Fix warning about using fabs() on integers. May 30, 2019
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 Add a usage example to reheader Jun 18, 2019
smpl_ilist.c
smpl_ilist.h Make the sample mapping work again with `annotate`. Fixes #123 Sep 18, 2018
tabix.c Build complete without plugins. Apr 15, 2019
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 Continuation of 2299ab6 Jul 15, 2019
vcfbuf.c Allow duplicate positions in both VCF and the TAB file with `call -C … Apr 18, 2019
vcfbuf.h Allow duplicate positions in both VCF and the TAB file with `call -C … Apr 18, 2019
vcfcall.c Merge pull request #609 from jkbonfield/jkb_win Jun 6, 2019
vcfcnv.c
vcfconcat.c Print a warning when `concat -l` drops a site. See #1039 Jun 24, 2019
vcfconvert.c Check return status of all *write() and *close() calls Jul 19, 2018
vcffilter.c Improve error messages. Resolves #951 and #925 Apr 15, 2019
vcfgtcheck.c Improve error messages. Resolves #951 and #925 Apr 15, 2019
vcfindex.c Check return status of all *write() and *close() calls Jul 19, 2018
vcfisec.c Merge pull request #609 from jkbonfield/jkb_win Jun 6, 2019
vcfmerge.c Do not rely on null-terminated strings in FORMAT. Fixes #1031 May 31, 2019
vcfnorm.c Improve error messages. Resolves #951 and #925 Apr 15, 2019
vcfplugin.c Merge pull request #609 from jkbonfield/jkb_win Jun 6, 2019
vcfquery.c Fix the nonfunctional `query -v` feature. Resolves #1054 Jul 16, 2019
vcfroh.c Improve error messages. Resolves #951 and #925 Apr 15, 2019
vcfsom.c Windows/Mingw/MSYS support. Apr 15, 2019
vcfsort.c Replace mktemp with mkdtemp Jul 18, 2019
vcfstats.c Add VAF indel stats and move plot-vcfstats to python3 Apr 24, 2019
vcfview.c Improve error messages. Resolves #951 and #925 Apr 15, 2019
vcmp.c Correctly transfer Number=G annotations, Mar 15, 2018
vcmp.h Correctly transfer Number=G annotations, Mar 15, 2018
version.c Grab errno earlier in error_errno() Jan 21, 2019
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

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