1+ ## Release 1.15 (21st February 2022)
2+
3+
4+ * New `bcftools head` subcommand for conveniently displaying the headers
5+ of a VCF or BCF file. Without any options, this is equivalent to
6+ `bcftools view --header-only --no-version` but more succinct and memorable.
7+
8+ * The `-T, --targets-file` option had the following bug originating in HTSlib code:
9+ when an uncompressed file with multiple columns CHR,POS,REF was provided, the
10+ REF would be interpreted as 0 gigabases (#1598)
11+
12+ Changes affecting specific commands:
13+
14+ * bcftools annotate
15+
16+ - In addition to `--rename-annots`, which requires a file with name mappings,
17+ it is now possible to do the same on the command line `-c NEW_TAG:=OLD_TAG`
18+
19+ - Add new option --min-overlap which allows to specify the minimum required
20+ overlap of intersecting regions
21+
22+ - Allow to transfer ALT from VCF with or without replacement using
23+ bcftools annotate -a annots.vcf.gz -c ALT file.vcf.gz
24+ bcftools annotate -a annots.vcf.gz -c +ALT file.vcf.gz
25+
26+ * bcftools convert
27+
28+ - Revamp of `--gensample`, `--hapsample` and `--haplegendsample` family of options
29+ which includes the following changes:
30+
31+ - New `--3N6` option to output/input the new version of the .gen file format,
32+ see https://www.cog-genomics.org/plink/2.0/formats#gen
33+
34+ - Deprecate the `--chrom` option in favor of `--3N6`. A simple `cut` command
35+ can be used to convert from the new 3*M+6 column format to the format printed
36+ with `--chrom` (`cut -d' ' -f1,3-`).
37+
38+ - The CHROM:POS_REF_ALT IDs which are used to detect strand swaps are required
39+ and must appear either in the "SNP ID" column or the "rsID" column. The column
40+ is autodetected for `--gensample2vcf`, can be the first or the second for
41+ `--hapsample2vcf` (depending on whether the `--vcf-ids` option is given), must be
42+ the first for `--haplegendsample2vcf`.
43+
44+ * bcftools csq
45+
46+ - Allow GFF files with phase column unset
47+
48+ * bcftools filter
49+
50+ - New `--mask`, `--mask-file` and `--mask-overlap` options to soft filter
51+ variants in regions (#1635)
52+
53+ * bcftools +fixref
54+
55+ - The `-m id` option now works also for non-dbSNP ids, i.e. not just `rsINT`
56+
57+ - New `-m flip-all` mode for flipping all sites, including ambiguous A/T and C/G sites
58+
59+ * bcftools isec
60+
61+ - Prevent segfault on sites filtered with -i/-e in all files (#1632)
62+
63+ * bcftools mpileup
64+
65+ - More flexible read filtering using the options
66+ --ls, --skip-all-set .. skip reads with all of the FLAG bits set
67+ --ns, --skip-any-set .. skip reads with any of the FLAG bits set
68+ --lu, --skip-all-unset .. skip reads with all of the FLAG bits unset
69+ --nu, --skip-any-unset .. skip reads with any of the FLAG bits unset
70+
71+ The existing synonymous options will continue to function but their use
72+ is discouraged
73+ --rf, --incl-flags STR|INT Required flags: skip reads with mask bits unset
74+ --ff, --excl-flags STR|INT Filter flags: skip reads with mask bits set
75+
76+ * bcftools query
77+
78+ - Make the `--samples` and `--samples-file` options work also in the `--list-samples`
79+ mode. Add a new `--force-samples` option which allows to proceed even when some of
80+ the requested samples are not present in the VCF (#1631)
81+
82+ * bcftools +setGT
83+
84+ - Fix a bug in `-t q -e EXPR` logic applied on FORMAT fields, sites with all
85+ samples failing the expression EXPR were incorrectly skipped. This problem
86+ affected only the use of `-e` logic, not the `-i` expressions (#1607)
87+
88+ * bcftools sort
89+
90+ - make use of the TMPDIR environment variable when defined
91+
92+ * bcftools +trio-dnm2
93+
94+ - The --use-NAIVE mode now also adds the de novo allele in FORMAT/VA
95+
96+
197## Release 1.14 (22nd October 2021)
298
399
4100Changes affecting the whole of bcftools, or multiple commands:
5101
6102* New `--regions-overlap` and `--targets-overlap` options which address
7- a long-standing design problem with subsetting VCF files by region.
103+ a long-standing design problem with subsetting VCF files by region.
8104 BCFtools recognize two sets of options, one for streaming (`-t/-T`) and
9105 one for index-gumping (`-r/-R`). They behave differently, the first
10106 includes only records with POS coordinate within the regions, the other
@@ -32,11 +128,11 @@ Changes affecting specific commands:
32128 by using `-c INFO/END`.
33129
34130 - add a new '.' modifier to control wheter missing values should be carried
35- over from a tab-delimited file or not. For example:
131+ over from a tab-delimited file or not. For example:
36132
37133 -c TAG .. adds TAG if the source value is not missing. If TAG
38134 exists in the target file, it will be overwritten
39-
135+
40136 -c .TAG .. adds TAG even if the source value is missing. This
41137 can overwrite non-missing values with a missing value
42138 and can create empty VCF fields (`TAG=.`)
@@ -165,7 +261,7 @@ Changes affecting specific commands:
165261* bcftools +fill-tags:
166262
167263 - Generalization and better support for custom functions that allow
168- adding new INFO tags based on arbitrary `-i, --include` type of
264+ adding new INFO tags based on arbitrary `-i, --include` type of
169265 expressions. For example, to calculate a missing INFO/DP annotation
170266 from FORMAT/AD, it is possible to use:
171267
@@ -229,7 +325,7 @@ Changes affecting specific commands:
229325
230326 - Atomization of AD and QS tags now correctly updates occurrences of duplicate
231327 alleles within different haplotypes
232-
328+
233329 - Fix a bug in atomization of Number=A,R tags
234330
235331* bcftools reheader:
@@ -241,7 +337,7 @@ Changes affecting specific commands:
241337 - A wider range of genotypes can be set by the plugin by allowing
242338 specifying custom genotypes. For example, to force a heterozygous
243339 genotype it is now possible to use expressions like:
244-
340+
245341 c:'m|M'
246342 c:0/1
247343 c:0
@@ -253,7 +349,7 @@ Changes affecting specific commands:
253349 - Better handling of ambiguous keys such as INFO/AF and CSQ/AD. The
254350 `-p, --annot-prefix` option is now applied before doing anything else
255351 which allows its use with `-f, --format` and `-c, --columns` options.
256-
352+
257353 - Some consequence field names may not constitute a valid tag name, such
258354 as "pos(1-based)". Newly field names are trimmed to exclude brackets.
259355
@@ -383,7 +479,7 @@ Changes affecting specific commands:
383479
384480* bcftools csq:
385481
386- - Fix a bug wich caused incorrect FORMAT/BCSQ formatting at sites with too
482+ - Fix a bug wich caused incorrect FORMAT/BCSQ formatting at sites with too
387483 many per-sample consequences
388484
389485 - Fix a bug which incorrectly handled the --ncsq parameter and could clash
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