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| Name: bcftools | Distribution: openSUSE Tumbleweed |
| Version: 1.19 | Vendor: openSUSE |
| Release: 1.1 | Build date: Wed Jan 3 15:12:40 2024 |
| Group: Productivity/Scientific/Other | Build host: i02-ch2b |
| Size: 2166520 | Source RPM: bcftools-1.19-1.1.src.rpm |
| Packager: https://bugs.opensuse.org | |
| Url: http://www.htslib.org/ | |
| Summary: Tools for manipulating variant calls in the Variant Call Format (VCF) | |
Package for the new BCFtools: a set of utilities that manipulate variant calls in the Variant Call Format (VCF) and its binary counterpart BCF. 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. BCFtools are meant as a faster replacement for most of the perl VCFtools commands.
MIT
* Wed Jan 03 2024 Stefan Brüns <stefan.bruens@rwth-aachen.de>
- Update to version 1.19
Too many changes to list, for details see
https://github.com/samtools/bcftools/releases/tag/1.19
- Update to version 1.18
Too many changes to list, for details see
https://github.com/samtools/bcftools/releases/tag/1.18
- Update to version 1.17
Too many changes to list, for details see
https://github.com/samtools/bcftools/releases/tag/1.17
* Fri Aug 26 2022 Jan Engelhardt <jengelh@inai.de>
- Update to release 1.16
* New plugin `bcftools +variant-distance` to annotate records
with distance to the nearest variant.
* The -i/-e filtering expression gained support for multiple
filters, e.g. `-i FILTER="A;B"`.
- Resolve "file packaged twice" rpmlint warnings
* Thu Apr 21 2022 Ferdinand Thiessen <rpm@fthiessen.de>
- Update to version 1.15.1
* bcftools annotate: New -H, --header-line convenience option to
pass a header line on command line
* bcftools csq: A list of consequence types supported by bcftools
csq has been added to the manual page.
* bcftools +fill-tags:
* Extend generalized functions so that FORMAT tags can be filled
as well
* Allow multiple custom functions in a single run.
* bcftools norm:
* Fix an assertion failure triggered when a faulty VCF file with
a '-' character in the REF allele was used with bcftools
norm --atomize.
* Fix the loss of phasing in half-missing genotypes in variant
atomization
* bcftools roh: Fix a bug that could result in an endless loop or
incorrect AF estimate when missing genotypes are present and
the --estimate-AF - option was used
* bcftools +split-vep: VEP fields with characters disallowed in
VCF tag names by the specification couldn't be queried.
- Update to version 1.15
* New bcftools head subcommand for conveniently displaying the
headers of a VCF or BCF file.
* The -T, --targets-file option had the following bug originating
in HTSlib code
* bcftools annotate:
* In addition to --rename-annots, which requires a file with
name mappings, it is now possible to do the same on the
command line -c NEW_TAG:=OLD_TAG
* Add new option --min-overlap which allows to specify the
minimum required overlap of intersecting regions
* Allow to transfer ALT from VCF with or without replacement
* bcftools convert:
* Revamp of --gensample, --hapsample and --haplegendsample
family of options
* New --3N6 option to output/input the new version of the .gen
file format
* Deprecate the --chrom option in favor of --3N6.
* The CHROM:POS_REF_ALT IDs which are used to detect strand
swaps are required and must appear either in the "SNP ID"
column or the "rsID" column.
* bcftools csq: Allow GFF files with phase column unset
* bcftools filter: New --mask, --mask-file and --mask-overlap
options to soft filter variants in regions
* bcftools +fixref
* The -m id option now works also for non-dbSNP ids
* New -m flip-all mode for flipping all sites
* bcftools isec: Prevent segfault on sites filtered with -i/-e
in all files
* bcftools mpileup: More flexible read filtering using the options
* bcftools query: Make the --samples and --samples-file options
work also in the --list-samples mode.
* bcftools +setGT: Fix a bug in -t q -e EXPR logic applied on
FORMAT fields, sites with all samples failing the expression
EXPR were incorrectly skipped.
* bcftools sort: make use of the TMPDIR environment variable
when defined
* bcftools +trio-dnm2: The --use-NAIVE mode now also adds the
de novo allele in FORMAT/VA
- Update to version 1.14
* New --regions-overlap and --targets-overlap options which
address a long-standing design problem with subsetting VCF
files by region.
* The --output-type option can be used to override the default
compression level
* bcftools annotate:
* when --set-id and --remove are combined, --set-id cannot use
tags deleted by --remove.
* while non-symbolic variation are uniquely identified by
POS,REF,ALT, symbolic alleles starting at the same position
were indistinguishable.
* add a new . modifier to control whether missing values should
be carried over from a tab-delimited file or not.
* bcftools +check-ploidy: by default missing genotypes are not
used when determining ploidy.
* bcftools concat: new --ligate-force and --ligate-warn options
for finer control of -l, --ligate behavior in imperfect overlaps.
* bcftools consensus: Apply mask even when the VCF has no notion
about the chromosome.
* bcftools +contrast: support for chunking within map/reduce
framework allowing to collect NASSOC counts even for empty
case/control sample sets
* bcftools csq:
* bug fix, compound indels were not recognised in some cases
* compound variants were incorrectly marked as 'inframe' even when
stop codon would occur before the frame was restored
* bug fix, FORMAT/BCSQ bitmasks could have been assigned incorrectly
to some samples at multiallelic sites, a superset of the correct
consequences would have been set
* bug fix, the upstream stop could be falsely assigned to all samples
in a multi-sample VCF even if the stop was relevant for a single
sample only
* further improve the detection of mismatching chromosome naming
(e.g. "chrX" vs "X") in the GFF, VCF and fasta files
* bcftools merge: keep (sum) INFO/AN,AC values when merging VCFs
with no samples
* bcftools mpileup: new --indel-size option which allows to increase
the maximum considered indel size considered, large deletions in
long read data are otherwise lost.
* bcftools norm:
* atomization now supports Number=A,R string annotations
* assign as many alternate alleles to genotypes at multiallelic
sites in the-m + mode, disregarding the phase.
* bcftools sort: increase accuracy of the --max-mem option limit,
previously the limit could be exceeded by more than 20%
* bcftools +trio-dnm: new --with-pAD option to allow processing of
VCFs without FORMAT/QS.
* bcftools view: the functionality of the option --compression-level
lost in 1.12 has been restored
- Update to version 1.13
* bcftools annotate:
* Fix rare a bug when INFO/END is present, all INFO fields are
removed with bcftools annotate -x INFO and BCF output is produced.
* Support for matching annotation line by ID, in addition to
CHROM,POS,REF, and ALT
* bcftools csq:
* When GFF and VCF/fasta use a different chromosome naming convention
no consequences would be added.
* Parametrize brief-predictions parameter to allow explicit number
of amino acids to be printed.
* bcftools +fill-tags:
* Generalization and better support for custom functions that allow
adding new INFO tags based on arbitrary -i, --include type of expressions.
* When FORMAT/GT is not present, the INFO/AF tag will be newly
calculated from INFO/AC and INFO/AN.
* bcftools gtcheck:
* Switch between FORMAT/GT or FORMAT/PL when one is (implicitly)
requested but only the other is available
* Improve diagnostics, printing warnings when a line cannot be
matched and the number of lines skipped for various reasons
* bcftools index: The program now accepts both data file name and
the index file name.
* bcftools isec: Always generate sites.txt with isec -p
* bcftools +mendelian: Consider only complete trios,
do not crash on sample name typos
* bcftools mpileup:
* New --seed option for reproducibility of subsampling code in HTSlib
* The SCR annotation which shows the number of soft-clipped reads
now correctly pools reads together regardless of the variant type.
* Major revamp of BAQ.
* Modified scale of Mann-Whitney U tests.
Newly INFO/*Z annotations will be printed
* bcftools norm:
* Fix Type=Flag output in norm --atomize
* Atomization must not discard ALT=. records
* Atomization of AD and QS tags now correctly updates occurrences
of duplicate alleles within different haplotypes
* Fix a bug in atomization of Number=A,R tags
* bcftools reheader: Add -T, --temp-prefix option
* bcftools +setGT: A wider range of genotypes can be set by the
plugin by allowing specifying custom genotypes.
* bcftools +split-vep:
* New -u, --allow-undef-tags option
* Better handling of ambiguous keys such as INFO/AF and CSQ/AD.
* Some consequence field names may not constitute a valid tag name,
such as "pos(1-based)".
* bcftools +tag2tag: New --QR-QA-to-QS option to convert annotations
generated by Freebayes to QS used by BCFtools
* bcftools +trio-dnm:
* Add support for sites with more than four alleles.
* New --use-NAIVE option for a naive DNM calling based solely on
FORMAT/GT and expected Mendelian inheritance.
* Fix behaviour to match the documentation, the --dnm-tag DNG option
now correctly outputs log scaled values by default, not phred scaled.
* Fix bug in VAF calculation, homozygous de novo variants were
incorrectly reported as having VAF=50%
* Fix arithmetic underflow which could lead to imprecise scores
and improve sensitivity in high coverage regions
* Allow combining --pn and --pns to set the noise thresholds independently
- Rebased use_python3.patch
- Drop python3 and perl build requirements, not needed, shbang of
executables can be patched anyway.
* Fri May 14 2021 Ferdinand Thiessen <rpm@fthiessen.de>
- Update to version 1.12
* The output file type is determined from the output file name
suffix, where available, so the -O/--output-type option is often
no longer necessary.
* Make F_MISSING in filtering expressions work for sites with
multiple ALT alleles
* Fix N_PASS and F_PASS to behave according to expectation when
reverse logic is used (#1397). This fix has the side effect of
query (or programs like +trio-stats) behaving differently with
these expressions, operating now in site-oriented rather than
sample-oriented mode.
* bcftools annotate:
* New --rename-annots option to help fix broken VCFs
* New -C option allows to read a long list of options from a file
to prevent very long command lines.
* New append-missing logic allows annotations to be added for
each ALT allele in the same order as they appear in the VCF.
* bcftools concat:
* Do not phase genotypes by mistake if they are not already
phased with -l
* bcftools consensus:
* New --mask-with, --mark-del, --mark-ins, --mark-snv options
* Symbolic <DEL> should have only one REF base. If there are
multiple, take POS+1 as the first deleted base.
* Make consensus work when the first base of the reference genome
is deleted.
* bcftools +contrast:
* The NOVELGT annotation was previously not added when requested.
* bcftools convert:
* Make the --hapsample and --hapsample2vcf options consistent with
each other and with the documentation.
* bcftools call:
* Revamp of call -G, previously sample grouping by population was
not truly independent and could still be influenced by the
presence of other sample groups.
* Optional addition of INFO/PV4 annotation with call -a INFO/PV4
* Remove generation of useless HOB and ICB annotation;
use +fill-tags -- -t HWE,ExcHet instead
* The call -f option was renamed to -a to (1) make it consistent
with mpileup and (2) to indicate that it includes both INFO and
FORMAT annotations
* bcftools csq:
* Fix a bug wich caused incorrect FORMAT/BCSQ formatting at sites
with too many per-sample consequences
* Fix a bug which incorrectly handled the --ncsq parameter and
could clash with reserved BCF values, consequently producing
truncated or even incorrect output of the %TBCSQ formatting
expression in bcftools query.
* bcftools +fill-tags:
* MAF definition revised for multiallelic sites, the second most
common allele is considered to be the minor allele
* New FORMAT/VAF, VAF1 annotations to set the fraction of
alternate reads provided FORMAT/AD is present
* bcftools gtcheck:
* support matching of a single sample against all other samples
in the file with -s qry:sample -s gt:-.
* bcftools merge:
* Make merge -R behavior consistent with other commands and pull
in overlapping records with POS outside of the regions
* Bug fix
* bcftools mpileup:
* Add new optional tag mpileup -a FORMAT/QS
* bcftools norm:
* New -a, --atomize functionality to decompose complex variants,
for example MNVs into consecutive SNVs
* New option --old-rec-tag to indicate the original variant
* bcftools query:
* Incorrect fields were printed in the per-sample output when
subset of samples was requested via -s/-S and the order of
samples in the header was different from the requested -s/-S order
* bcftools +prune:
* New options --random-seed and --nsites-per-win-mode
* bcftools +split-vep:
* Transcript selection now works also on the raw CSQ/BCSQ annotation.
* Bug fix, samples were dropped on VCF input and VCF/BCF output
* bcftools stats:
* Changes to QUAL and ts/tv plotting stats: avoid capping QUAL to
predefined bins, use an open-range logarithmic binning instead
* plot dual ts/tv stats: per quality bin and cumulative as if
threshold applied on the whole dataset
* bcftools +trio-dnm2:
* Major revamp of +trio-dnm plugin, which is now deprecated
and replaced by +trio-dnm2.
* The original trio-dnm calling model used genotype likelihoods
(PLs) as the input for calling.
* This new version also implements the DeNovoGear model.
* For more details see http://samtools.github.io/bcftools/trio-dnm.pdf
- Update use_python3.patch
* Thu May 13 2021 Ferdinand Thiessen <rpm@fthiessen.de>
- Update to version 1.11
* Breaking change in -i/-e expressions on the FILTER column.
The new behaviour is:
Expression Result
FILTER="A" Exact match, for example "A;B" does not pass
FILTER!="A" Exact match, for example "A;B" does pass
FILTER~"A" Both "A" and "A;B" pass
FILTER!~"A" Neither "A" nor "A;B" pass
* Fix in commutative comparison operators, in some cases reversing
sides would produce incorrect results
* Better support for filtering on sample subsests
* bcftools annotate:
* Previously it was not possible to use --columns =TAG with INFO
tags and the --merge-logic feature was restricted to tab files
with BEG,END columns, now extended to work also with REF,ALT.
* Make annotate -TAG/+TAG work also with FORMAT fields.
* ID and FILTER can be transferred to INFO and ID can be populated
from INFO.
* bcftools consensus:
* Fix in handling symbolic deletions and overlapping variants.
* Fix --iupac-codes crash on REF-only positions with ALT=".".
* Fix --chain crash
* Preserve the case of the genome reference.
* Add new -a, --absent option which allows to set positions with
no supporting evidence to "N" (or any other character).
* bcftools convert:
* The option --vcf-ids now works also with -haplegendsample2vcf.
* New option --keep-duplicates
* bcftools csq:
* Add misc/gff2gff.py script for conversion between various
flavors of GFF files. The initial commit supports only one type
* Add missing consequence types.
* Allow overlapping CDS to support ribosomal slippage.
* bcftools +fill-tags:
* Added new annotations: INFO/END, TYPE, F_MISSING.
* bcftools filter:
* Make --SnpGap optionally filter also SNPs close to other variant
types.
* bcftools gtcheck:
* Complete revamp of the command. The new version is faster and allows
N:M sample comparisons, not just 1:N or NxN comparisons. Some
functionality was lost (plotting and clustering) but may be added back
on popular demand.
* bcftools +mendelian:
* Revamp of user options, output VCFs with mendelian errors annotation,
read PED files
* bcftools merge:
* Update headers when appropriate with the '--info-rules *:join'
INFO rule.
* Local alleles merging that produce LAA and LPL when requested, a
draft implementation of samtools/hts-specs#434
* New --no-index which allows to merge unindexed files.
* Fixes in gVCF merging.
* bcftools norm:
* Fixes in --check-ref s reference setting features with non-ACGT bases.
* New --keep-sum switch to keep vector sum constant when splitting
multiallelics.
* bcftools +prune:
* Extend to allow annotating with various LD metrics: r^2, Lewontin's D'
* bcftools query:
* New %N_PASS() formatting expression to output the number of samples
that pass the filtering expression.
* bcftools reheader:
* Improved error reporting to prevent user mistakes.
* bcftools roh:
* The --AF-file description incorrectly suggested "REF\tALT"
instead of the correct "REF,ALT".
* RG lines could have negative length.
* new --include-noalt option to allow also ALT=. records.
* bcftools scatter:
* New plugin intended as a convenient inverse to concat
* bcftools +split:
* New --groups-file option for more flexibility of defining
desired output
* New --hts-opts option to reduce required memory by reusing
one output
header and allow overriding the default hFile's block size
* Add support for multisample output and sample renaming
* bcftools +split-vep:
* Add default types (Integer, Float, String) for VEP subfields
and make --columns - extract all subfields into INFO tags
in one go.
* Tue Feb 25 2020 Pierre Bonamy <flyos@mailoo.org>
- Changed python dependencies from python3 to python3-base and
python3-matplotlib
* Wed Feb 12 2020 Todd R <toddrme2178@gmail.com>
- Add use_python3.patch to switch from python2 to python3
* Wed Feb 05 2020 Todd R <toddrme2178@gmail.com>
- Update to 1.10.2
* This release fixes crashes reported on files including integer
INFO tags with values outside the range officially supported
by VCF. It also fixes a bug where invalid BCF files would be
created if such values were present.
- Update to 1.10.0
+ Numerous bug fixes, usability improvements and sanity checks were added to prevent common user errors.
+ The -r, --regions (and -R, --regions-file) option should never create unsorted VCFs or duplicates records again. This also fixes rare cases where a spanning deletion makes a subsequent record invisible to bcftools isec and other commands.
+ Additions to filtering and formatting expressions
* support for the spanning deletion alternate allele (ALT=*)
* new ILEN filtering expression to be able to filter by indel length
* new MEAN, MEDIAN, MODE, STDEV, phred filtering functions
* new formatting expression %PBINOM (phred-scaled binomial probability), %INFO (the whole INFO column), %FORMAT (the whole FORMAT column), %END (end position of the REF allele), %END0 (0-based end position of the REF allele), %MASK (with multiple files indicates the presence of the site in other files)
+ New plugins
* +gvcfz: compress gVCF file by resizing gVCF blocks according to specified criteria
* +indel-stats: collect various indel-specific statistics
* +parental-origin: determine parental origin of a CNV region
* +remove-overlaps: remove overlapping variants.
* +split-vep: query structured annotations such INFO/CSQ created by bcftools/csq or VEP
* +trio-dnm: screen variants for possible de-novo mutations in trios
+ annotate
* new -l, --merge-logic option for combining multiple overlapping regions
+ call
* new bcftools call -G, --group-samples option which allows grouping samples into populations and applying the HWE assumption within but not across the groups.
+ csq
* significant reduction of memory usage in the local -l mode for VCFs with thousands of samples and 20% reduction in the non-local haplotype-aware mode.
* fixes a small memory leak and formatting issue in FORMAT/BCSQ at sites with many consequences
* do not print protein sequence of start_lost events
* support for "start_retained" consequence
* support for symbolic insertions (ALT="<INS...>"), "feature_elongation" consequence
* new -b, --brief-predictions option to output abbreviated protein predictions.
+ concat
* the --naive command now checks header compatibility when concatenating multiple files.
+ consensus
* add a new -H, --haplotype 1pIu/2pIu feature to output first/second allele for phased genotypes and the IUPAC code for unphased genotypes
* new -p, --prefix option to add a prefix to sequence names on output
+ +contrast
* added support for Fisher's test probability and other annotations
+ +fill-from-fasta
* new -N, --replace-non-ACGTN option
+ +dosage
* fix some serious bugs in dosage calculation
+ +fill-tags
* extended to perform simple on-the-fly calculations such as calculating INFO/DP from FORMAT/DP.
+ merge
* add support for merging FORMAT strings
* bug fixed in gVCF merging
+ mpileup
* a new optional SCR annotation for the number of soft-clipped reads
+ reheader
* new -f, --fai option for updating contig lines in the VCF header
+ +trio-stats
* extend output to include DNM homs and recurrent DNMs
+ VariantKey support
* Thu Sep 06 2018 flyos@mailoo.org
- Update to 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
* Thu Jul 12 2018 flyos@mailoo.org
- Cleaned spec file using spec-cleaner
- Update to 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
* `-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
* 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 (#639) - see the man page for details.
* `csq`: relax some GFF3 parsing restrictions to enable using Ensembl
GFF3 files for plants (#667)
* `stats`: add further documentation to output stats files (#316) and
include haploid counts in per-sample output (#671).
* `plot-vcfstats`: further fixes for Python3 (@nsoranzo, #645, #666).
* `query` bugfix (#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 (#636)
* `convert --gvcf2vcf` bugfix (#641)
* `+mendelian`: recognize some mendelian inconsistencies that were
being missed (@oronnavon, #660), also add support for multiallelic
sites and sex chromosomes.
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Fabrice Bellet, Wed Nov 13 00:41:02 2024