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flesh out NEWS file for upcoming 1.4 including some previous release …
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| Original file line number | Diff line number | Diff line change |
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| @@ -1,14 +1,209 @@ | ||
| Noteworthy changes in release 1.4 | ||
| ## Noteworthy changes in release 1.4 (DD Mmmmm 2016) | ||
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| * The `mpileup` command moved from samtools to bcftools. The basic | ||
| functionality remains unchanged and so does most of the command line | ||
| options, but there are differences one should be aware of: | ||
| Two new commands - `mpileup` and `csq`: | ||
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| * 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. | ||
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| 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: | ||
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| - The option `samtools mpileup -t, --output-tags` changed to `bcftools | ||
| mpileup -a, --annotate`. The short -t option has a different meaning | ||
| in bcftools, consistent with the rest of bcftools commands. | ||
| mpileup -a, --annotate` to avoid conflict with the `-t, --targets` | ||
| option common across other bcftools commands. | ||
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| - `-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. | ||
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| - `-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. | ||
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| - The `-f, --fasta-ref` option is now required by default to help avoid user | ||
| errors. Can be diabled using `--no-reference`. | ||
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| - The option `-d, --depth .. max per-file depth` now behaves as expected | ||
| amd according to the documentation, and prints a meaningful diagnostics. | ||
| and according to the documentation, and prints a meaningful diagnostics. | ||
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| - The `-S, --samples-file` can be used to rename samples on the fly. See man | ||
| page for details. | ||
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| - The `-G, --read-groups` functionality has been extended to allow | ||
| reassignment, grouping and exclusion of readgroups. See man page for | ||
| details. | ||
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| - The `-l, --positions` replaced by the `-t, --targets` and | ||
| `-T, --targets-file` options to be consistent with other bcftools | ||
| commands. | ||
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| - gVCF output is supported. Per-sample gVCFs created by mpileup can be | ||
| merged using `bcftools merge --gvcf`. | ||
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| - 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. | ||
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| - Several speedups thanks to @jkbonfield (cf3a55a). | ||
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| * `csq`: New command for haplotype-aware variant consequence calling. | ||
| See man page and [paper](https://www.ncbi.nlm.nih.gov/pubmed/28205675). | ||
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| Updates, improvements and bugfixes for many other commands: | ||
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| * `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 (#469). Bugfixes (#428). | ||
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| * `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 (#449, 7c56870). `PLs>=256` allowed in | ||
| `call -m`. Bugfixes (#436). | ||
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| * `concat --naive` now works with vcf.gz in addition to bcf files. | ||
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| * `consensus`: handle variants overlapping region boundaries (#400). | ||
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| * `convert`: gvcf2vcf support for mpileup and GATK. new `--sex` option to | ||
| assign sex to be used in certain output types (#500). Large speedup of | ||
| `--hapsample` and `--haplegendsample` (e8e369b) especially with `--threads` | ||
| option enabled. Bugfixes (#460). | ||
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| * `cnv`: improvements to output (be8b378). | ||
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| * `filter`: bugfixes (#406). | ||
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| * `gtcheck`: improved cross-check mode (#441). | ||
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| * `index` can now specify the path to the output index file. Also, gains the | ||
| `--threads` option. | ||
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| * `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 (#296, #361, #401, | ||
| #408, #412). | ||
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| * `norm`: Bugfixes (#385,#452,#439), more informative error messages (#364). | ||
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| * `query`: `%END` plus `%POS0`, `%END0` (0-indexed) support - allows easy BED | ||
| format output (#479). `%TBCSQ` for use with the new `csq` command. Bugfixes | ||
| (#488,#489). | ||
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| * `plugin`: A number of new plugins: | ||
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| - `GTsubset` (thanks to @dlaehnemann) | ||
| - `ad-bias` | ||
| - `af-dist` | ||
| - `fill-from-fasta` | ||
| - `fixref` | ||
| - `guess-ploidy` (deprecates `vcf2sex` plugin) | ||
| - `isecGT` | ||
| - `trio-switch-rate` | ||
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| and changes to existing plugins: | ||
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| - `tag2tag`: Added `gp-to-gt`, `pl-to-gl` and `--threshold` options and | ||
| bugfixes (#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. (#503). HWE tag added as an option. | ||
| - `mendelian`: Bugfix (#566). | ||
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| * `reheader`: allow muiltispace delimiters in `--samples` option. | ||
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| * `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. | ||
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| * `stats`: Bugfixes (16414e6), new options `-af-bins` and `-af-tags` to control | ||
| allele frequency binning of output. Per-sample genotype concordance tables | ||
| added (#477). | ||
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| * `view -a, --trim-alt-alleles` various bugfixes for missing data and more | ||
| informative errors should now be given on failure to pinpoint problems. | ||
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| General changes: | ||
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| * Timestamps are now added to header lines summarising the command (#467). | ||
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| * 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. | ||
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| * Changes to genotype filtering with `-i, --include` and `-e, --exclude` (#454). | ||
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| ## Noteworthy changes in release 1.3.1 (22 April 2016) | ||
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| * The `concat` command has a new `--naive` option for faster operations on | ||
| large BCFs (PR #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 (#378). | ||
| * Various bug fixes and improvements to the `annotate` (#365), `call` (#366), | ||
| `index` (#367), `norm` (#368, #385), `reheader` (#356), and `roh` (#328) | ||
| commands, and to the `fill-tags` (#345) and `tag2tag` (#394) plugins. | ||
| * Clarified documentation of `view` filter options, and of the | ||
| `--regions-file` and `--targets-file` options (#357, #411). | ||
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| ## Noteworthy changes in release 1.3 (15 December 2016) | ||
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| * `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` and `polysomy`: new commands for detecting CNVs, aneuploidy, and | ||
| contamination from SNP genotyping data. | ||
| * various new options, plugins, and bug fixes, including #84, #201, #204, | ||
| #205, #208, #211, #222, #225, #242, #243, #249, #282, #285, #289, #302, | ||
| #311, #318, #336, and #338. | ||
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| ## Noteworthy changes in release 1.2 (2 February 2016) | ||
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| * new `bcftools consensus` command | ||
| * new `bcftools annotate` plugins: fixploidy, vcf2sex, tag2tag | ||
| * more features in `bcftools convert` command, amongst others new | ||
| `--hapsample` function (thanks to Warren Kretzschmar @wkretzsch) | ||
| * support for complements in `bcftools annotate --remove` | ||
| * support for `-i`/`-e` filtering expressions in `bcftools isec` | ||
| * improved error reporting | ||
| * `bcftools call` | ||
| - the default prior increased from `-P 1e-3` to `-P 1.1e-3`, some clear | ||
| calls were missed with default settings previously | ||
| - support for the new symbolic allele `<*>` | ||
| - support for `-f GQ` | ||
| - bug fixes, such as: proper trimming of DPR tag with `-c`; the `-A` switch | ||
| does not add back records removed by `-v` and the behaviour has been made | ||
| consistent with `-c` and `-m` | ||
| * many bug fixes and improvements, such as | ||
| - bug in filtering, FMT & INFO vs INFO & FMT | ||
| - fixes in `bcftools merge` | ||
| - filter update AN/AC with `-S` | ||
| - isec outputs matching records for both VCFs in the Venn mode | ||
| - annotate considers alleles when working with `Number=A,R` tags | ||
| - new `--set-id` feature for annotate | ||
| - `convert` can be used similarly to `view` |