bcftools release 1.9:

* `annotate`

    - REF and ALT columns can be now transferred from the annotation
      file.

    - fixed bug when setting vector_end values.

* `consensus`

    - new -M option to control output at missing genotypes

    - variants immediately following insersions should not be
      skipped.  Note however, that the current fix requires
      normalized VCF and may still falsely skip variants adjacent
      to multiallelic indels.

    - bug fixed in -H selection handling

* `convert`

    - the --tsv2vcf option now makes the missing genotypes diploid,
      "./." instead of "."

    - the behavior of -i/-e with --gvcf2vcf changed. Previously only
      sites with FILTER set to "PASS" or "." were expanded and the
      -i/-e options dropped sites completely. The new behavior is to
      let the -i/-e options control which records will be expanded.
      In order to drop records completely, one can stream through
      "bcftools view" first.

* `csq`

    - since the real consequence of start/splice events are not
      known, the aminoacid positions at subsequent variants should
      stay unchanged

    - add `--force` option to skip malformatted transcripts in GFFs
      with out-of-phase CDS exons.

* `+dosage`: output all alleles and all their dosages at multiallelic
  sites

* `+fixref`: fix serious bug in -m top conversion

* `-i/-e` filtering expressions:

    - add two-tailed binomial test

    - add functions N_PASS() and F_PASS()

    - add support for lists of samples in filtering expressions,
      with many samples it was impractical to list them all on
      the command line. Samples can be now in a file as, e.g.,
      GT[@samples.txt]="het"

    - allow multiple perl functions in the expressions and some bug
      fixes

    - fix a parsing problem, '@' was not removed from '@filename'
      expressions

* `mpileup`: fixed bug where, if samples were renamed using the `-G`
  (`--read-groups`) option, some samples could be omitted from the
  output file.

* `norm`: update INFO/END when normalizing indels

* `+split`: new -S option to subset samples and to use custom file
  names instead of the defaults

* `+smpl-stats`: new plugin

* `+trio-stats`: new plugin

* Fixed build problems with non-functional configure script produced
  on some platforms

bcftools release 1.8:

* `-i, -e` filtering: Support for custom perl scripts

* `+contrast`: New plugin to annotate genotype differences between
  groups of samples

* `+fixploidy`: New options for simpler ploidy usage

* `+setGT`: Target genotypes can be set to phased by giving `--new-gt
  p`

* `run-roh.pl`: Allow to pass options directly to `bcftools roh`

* Number of bug fixes

BCFtools release 1.7: improved filtering; many other upgrades

* `-i, -e` filtering: Major revamp, improved filtering by FORMAT fields
  and missing values. New GT=ref,alt,mis etc keywords, check the
  documenation for details.

* `query`: Only matching expression are printed when both the -f and -i/-e
  expressions contain genotype fields. Note that this changes the original
  behavior. Previously all samples were output when one matching sample was
  found. This functionality can be achieved by pre-filtering with view and
  then streaming to query. Compare
        bcftools query -f'[%CHROM:%POS %SAMPLE %GT\n]' -i'GT="alt"' file.bcf
  and
        bcftools view -i'GT="alt"' file.bcf -Ou | bcftools query -f'[%CHROM:%POS %SAMPLE %GT\n]'

* `annotate`: New -k, --keep-sites option

* `consensus`: Fix --iupac-codes output

* `csq`: Homs always considered phased and other fixes

* `norm`: Make `-c none` work and remove `query -c`

* `roh`: Fix errors in the RG output

* `stats`: Allow IUPAC ambiguity codes in the reference file; report the
  number of missing genotypes

* `+fill-tags`: Add ExcHet annotation

* `+setGt`: Fix bug in binom.test calculation, previously it worked only
  for nAlt<nRef!

* `+split`: New plugin to split a multi-sample file into single-sample
  files in one go

* Improve python3 compatibility in plotting scripts

BCFtools release 1.6: sort command; filtering and other improvements

* New `sort` command.

* New options added to the `consensus` command. Note that the `-i, --iupac`
  option has been renamed to `-I, --iupac`, in favor of the standard 
  `-i, --include`.

* Filtering expressions (`-i/-e`): support for `GT=<type>` expressions and
  for lists and ranges (samtools#639) - see the man page for details.

* `csq`: relax some GFF3 parsing restrictions to enable using Ensembl
  GFF3 files for plants (samtools#667)

* `stats`: add further documentation to output stats files (samtools#316) and
  include haploid counts in per-sample output (samtools#671).

* `plot-vcfstats`: further fixes for Python3 (@nsoranzo, samtools#645, samtools#666).

* `query` bugfix (samtools#632)

* `+setGT` plugin: new option to set genotypes based on a two-tailed binomial
  distribution test. Also, allow combining `-i/-e` with `-t q`.

* `mpileup`: fix typo (samtools#636)

* `convert --gvcf2vcf` bugfix (samtools#641)

* `+mendelian`: recognize some mendelian inconsistencies that were
  being missed (@oronnavon, samtools#660), also add support for multiallelic
  sites and sex chromosomes.

## Release 1.5 (June 2017)

* Added autoconf support to bcftools. See `INSTALL` for more details.

* `norm`: Make norm case insensitive (samtools#601). Trim the reference allele (samtools#602).

* `mpileup`: fix for misreported indel depths for reads containing adjacent
  indels (3c1205c).

* `plot-vcfstats`: Open stats file in text mode, not binary (samtools#618).

* `fixref` plugin: Allow multiallelic sites in the `-i, --use-id reference`.
  Also flip genotypes, not just REF/ALT!

* `merge`: fix gVCF merge bug when last record on a chromosome opened a
  gVCF block (samtools#616)

* New options added to the ROH plotting script.

* `consensus`: Properly flush chain info (samtools#606, thanks to @krooijers).

* New `+prune` plugin for pruning sites by LD (R2) or maximum number of
  records within a window.

* New N_MISSING, F_MISSING (number and fraction misssing) filtering
  expressions.

* Fix HMM initilization in `roh` when snapshots are used in multiple
  chromosome VCF.

* Fix buffer overflow (samtools#607) in `filter`.

## Release 1.4.1 (8 May 2017)

* `roh`: Fixed malfunctioning options `-m, --genetic-map` and `-M, --rec-rate`,
  and newly allowed their combination. Added a convenience wrapper `misc/run-roh.pl`
  and an interactive script for visualizing the calls `misc/plot-roh.py`.

* `csq`: More control over warning messages (samtools#585).

* Portability improvements (samtools#587). Still work to be done on this front.

* Add support for breakends to `view`, `norm`, `query` and filtering (samtools#592).

* `plot-vcfstats`: Fix for python 2/3 compatibility (samtools#593).

* New `-l, --list` option for `+af-dist` plugin.

* New `-i, --use-id` option for `+fix-ref` plugin.

* Add `--include/--exclude` options to `+guess-ploidy` plugin.

* New `+check-sparsity` plugin.

* Miscellaneous bugfixes for samtools#575, samtools#584, samtools#588, samtools#599, samtools#535.

Release 1.4 (13 March 2017)

Two new commands - `mpileup` and `csq`:

* The `mpileup` command has been imported from samtools to bcftools. The
  reasoning behind this is that bcftools calling is intimately tied to mpileup
  and any changes to one, often requires changes to the other. Only the
  genotype likelihood (BCF output) part of mpileup has moved to bcftools,
  while the textual pileup output remains in samtools. The BCF output option
  in `samtools mpileup` will likely be removed in a release or two or when
  changes to `bcftools call` are incompatible with the old mpileup output.

  The basic mpileup functionality remains unchanged as do most of the command
  line options, but there are some differences and new features that one
  should be aware of:

  - The option `samtools mpileup -t, --output-tags` changed to `bcftools
    mpileup -a, --annotate` to avoid conflict with the `-t, --targets`
    option common across other bcftools commands.

  - `-O, --output-BP` and `-s, --output-MQ` are no longer used as they are
    only for textual pipelup output, which is not included in `bcftools
    mpileup`. `-O` short option reassigned to `--output-type` and `-s`
    reassigned to `--samples` for consistency with other bcftools commands.

  - `-g, --BCF`, `-v, --VCF`, and ` -u, --uncompressed` options from
    `samtools mpileup` are no longer used, being replaced by the
    `-O, --output-type` option common to other bcftools commands.

  - The `-f, --fasta-ref` option is now required by default to help avoid user
    errors. Can be diabled using `--no-reference`.

  - The option `-d, --depth .. max per-file depth` now behaves as expected
    and according to the documentation, and prints a meaningful diagnostics.

  - The `-S, --samples-file` can be used to rename samples on the fly. See man
    page for details.

  - The `-G, --read-groups` functionality has been extended to allow
    reassignment, grouping and exclusion of readgroups. See man page for
    details.

  - The `-l, --positions` replaced by the `-t, --targets` and
    `-T, --targets-file` options to be consistent with other bcftools
    commands.

  - gVCF output is supported. Per-sample gVCFs created by mpileup can be
    merged using `bcftools merge --gvcf`.

  - Can generate mpileup output on multiple (indexed) regions using the
    `-r, --regions` and `-R, --regions-file` options. In samtools, one
    was restricted to a single region with the `-r, --region` option.

  - Several speedups thanks to @jkbonfield (cf3a55a).

* `csq`: New command for haplotype-aware variant consequence calling.
  See man page and [paper](https://www.ncbi.nlm.nih.gov/pubmed/28205675).


Updates, improvements and bugfixes for many other commands:

* `annotate`: `--collapse` option added. `--mark-sites` now works with
  VCF files rather than just tab-delimited files. Now possible to annotate
  a subset of samples from tab file, not just VCF file (samtools#469). Bugfixes (samtools#428).

* `call`: New option `-F, --prior-freqs` to take advantage of prior knowledge
    of population allele frequencies. Improved calculation of the QUAL score
    particularly for REF sites (samtools#449, 7c56870). `PLs>=256` allowed in
    `call -m`. Bugfixes (samtools#436).

* `concat --naive` now works with vcf.gz in addition to bcf files.

* `consensus`: handle variants overlapping region boundaries (samtools#400).

* `convert`: gvcf2vcf support for mpileup and GATK. new `--sex` option to
  assign sex to be used in certain output types (samtools#500). Large speedup of
  `--hapsample` and `--haplegendsample` (e8e369b) especially with `--threads`
  option enabled. Bugfixes (samtools#460).

* `cnv`: improvements to output (be8b378).

* `filter`: bugfixes (samtools#406).

* `gtcheck`: improved cross-check mode (samtools#441).

* `index` can now specify the path to the output index file. Also, gains the
   `--threads` option.

* `merge`: Large overhaul of `merge` command including support for merging
  gVCF files created by `bcftools mpileup --gvcf` with the new `-g, --gvcf`
  option. New options `-F` to control filter logic and `-0` to set missing
  data to REF. Resolved a number of longstanding issues (samtools#296, samtools#361, samtools#401,
  samtools#408, samtools#412).

* `norm`: Bugfixes (samtools#385,samtools#452,samtools#439), more informative error messages (samtools#364).

* `query`: `%END` plus `%POS0`, `%END0` (0-indexed) support - allows easy BED
  format output (samtools#479). `%TBCSQ` for use with the new `csq` command. Bugfixes
  (samtools#488,samtools#489).

* `plugin`: A number of new plugins:

  - `GTsubset` (thanks to @dlaehnemann)
  - `ad-bias`
  - `af-dist`
  - `fill-from-fasta`
  - `fixref`
  - `guess-ploidy` (deprecates `vcf2sex` plugin)
  - `isecGT`
  - `trio-switch-rate`

  and changes to existing plugins:

  - `tag2tag`: Added `gp-to-gt`, `pl-to-gl` and `--threshold` options and
    bugfixes (samtools#475).
  - `ad-bias`: New `-d` option for minimum depth.
  - `impute-info`: Bugfix (49a9eaf).
  - `fill-tags`:  Added ability to aggregate tags for sample subgroups, thanks
    to @mh11. (samtools#503). HWE tag added as an option.
  - `mendelian`: Bugfix (samtools#566).

* `reheader`: allow muiltispace delimiters in `--samples` option.

* `roh`: Now possible to process multiple samples at once. This allows
  considerable speedups for files with thousands of samples where the cost of
  HMM is neglibible compared to I/O and decompressing. In order to fit tens of
  thousands samples in memory, a sliding HMM can be used (new `--buffer-size`
  option). Viterbi training now uses Baum-Welch algorithm, and works much
  better. Support for gVCFs or FORMAT/PL tags. Added `-o, output` and
  `-O, --output-type` options to control output of sites or regions
  (compression optional). Many bugs fixed - do not segfault on missing PL
  values anymore, a typo in genetic map calculation resulted in a slowdown and
  incorrect results.

* `stats`: Bugfixes (16414e6), new options `-af-bins` and `-af-tags` to control
  allele frequency binning of output. Per-sample genotype concordance tables
  added (samtools#477).

* `view -a, --trim-alt-alleles` various bugfixes for missing data and more
  informative errors should now be given on failure to pinpoint problems.


General changes:

* Timestamps are now added to header lines summarising the command (samtools#467).

* Use of the `--threads` options should be faster across the board thanks to
  changes in HTSlib meaning meaning threads are now shared by the compression
  and decompression calls.

* Changes to genotype filtering with `-i, --include` and `-e, --exclude` (samtools#454).

BCFtools release 1.3.1: bug fixes, new GTisec plugin

* The concat command has a new --naive option for faster operations
  on large BCFs (PR samtools#359).

* GTisec: new plugin courtesy of David Laehnemann (@dlaehnemann) to count
  genotype intersections across all possible sample subsets in a VCF file.

* Numerous VCF parsing fixes.

* Build fix: peakfit.c now builds correctly with GSL v2 (samtools#378).

* Various bug fixes and improvements to the annotate (samtools#365), call (samtools#366),
  index (samtools#367), norm (samtools#368, samtools#385), reheader (samtools#356), and roh (samtools#328) commands,
  and to the fill-tags (samtools#345) and tag2tag (samtools#394) plugins.

* Clarified documentation of view filter options, and of the --regions-file
  and --targets-file options (samtools#357, samtools#411).

BCFtools release 1.3: various new options, plugins, bug fixes

* bcftools call has new options --ploidy and --ploidy-file to make handling
  sample ploidy easier. See man page for details.

* stats: -i/-e short options changed to -I/-E to be consistent with the
  filtering -i/-e (--include/--exclude) options used in other tools.

* general --threads option to control the number of output compression
  threads used when outputting compressed VCF or BCF.

* cnv & polysomy: new commands for detecting CNVs, aneuploidy, and
  contamination from SNP genotyping data.

* various new options, plugins, and bug fixes, including samtools#84, samtools#201, samtools#204,
  samtools#205, samtools#208, samtools#211, samtools#222, samtools#225, samtools#242, samtools#243, samtools#249, samtools#282, samtools#285, samtools#289, samtools#302,
  samtools#311, samtools#318, samtools#336, and samtools#338.

New consensus command, new annotate and convert features