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## Release a.b
Changes affecting specific commands:
* bcftools consensus
- Add new --regions-overlap option which allows to take into account overlapping deletions
that start out of the fasta file target region.
* bcftools isec
- Add new option `-l, --file-list` to read the list of file names from a file
* bcftools merge
- Add new option `--force-single` to support single-file edge case (#2100)
* bcftools norm
- Change the order of atomization and multiallelic splitting (when both -a,-m are given)
from "atomize first, then split" to "split first, then atomize". This usually results
in a simpler VCF representation. The previous behaviour can be achieved by explicitly
streaming the output of the --atomize command into the --multiallelics splitting command.
- Fix Type=String multiallelic splitting for Number=A,R,G tags with incorrect number
of values.
- Merging into multiallelic sites with `bcftools norm -m +indels` did not work. This is
now fixed and the merging is now more strict about variant types, for example complex
events, such as AC>TGA, are not considered as indels anymore (#2084)
* bcftools reheader
- Allow reading the input file from a stream with --fai (#2088)
* bcftools +setGT
- Support for custom genotypes based on the allele with higher depth, such
as `--new-gt c:0/X` custom genotypes (#2065)
* bcftools +split-vep
- When only one of the tags is present, automatically choose INFO/BCSQ (the default
tag name produced by `bcftools csq`) or INFO/CSQ (produced by VEP). When both
tags are present, use the default INFO/CSQ.
- Transcript selection by MANE, PICK, and user-defined transcripts, for example
--select CANONICAL=YES
--select MANE_SELECT!=""
--select PolyPhen~probably_damaging
- Select all matching transcripts via --select, not just one
- Change automatic type parsing of VEP fields DNA_position, CDS_position, and Protein_position
from Integer to String, as it can be of the form "8586-8599/9231". The type Integer can be
still enforced with `-c cDNA_position:int,CDS_position:int,Protein_position:int`.
- Recognize `-c field:str`, not just `-c field:string`, as advertised in the usage page
- Fix a bug which made filtering expression containing missing values crash (#2098)
* bcftools stats
- When GT is missing but AD is present, the program determines the alternate allele from AD.
However, if the AD tag has incorrect number of values, the program would exit with an error
printing "Requested allele outside valid range". This is now fixed by taking into account
the actual number of ALT alleles.
* bcftools +tag2tag
- Support for conversion from tags using localized alleles (e.g. LPL, LAD) to the family of
standard tags (PL, AD)
* bcftools +trio-dnm2
- Extend --strictly-novel to exclude cases where the non-Mendelian allele
is the reference allele. The change is motivated by the observation that
this class of variants is enriched for errors (especially for indels),
and better corresponds with the option name.
## Release 1.19 (12th December 2023)
Changes affecting the whole of bcftools, or multiple commands:
* Filtering expressions can be given a file with list of strings to match, this
was previously possible only for the ID column. For example
ID=@file .. selects lines with ID present in the file
INFO/TAG=@file.txt .. selects lines where TAG has a string value listed in the file
INFO/TAG!=@file.txt .. TAG must not have a string value listed in the file
Allow to query REF,ALT columns directly, for example
-e 'REF="N"'
Changes affecting specific commands:
* bcftools annotate
- Fix `bcftools annotate --mark-sites`, VCF sites overlapping regions in a BED file
were not annotated (#1989)
- Add flexibility to FILTER column transfers and allow transfers within the same file,
across files, and in combination. For examples see
http://samtools.github.io/bcftools/howtos/annotate.html#transfer_filter_to_info
* bcftools call
- Output MIN_DP rather than MinDP in gVCF mode
- New `-*, --keep-unseen-allele` option to output the unobserved allele <*>,
intended for gVCF.
* bcftools head
- New `-s, --samples` option to include the #CHROM header line with samples.
* bcftools gtcheck
- Add output options `-o, --output` and `-O, --output-type`
- Add filtering options `-i, --include` and `-e, --exclude`
- Rename the short option `-e, --error-probability` from lower case to upper
case `-E, --error-probability`
- Changes to the output format, replace the DC section with DCv2:
- adds a new column for the number of matching genotypes
- The --error-probability is newly interpreted as the probability of erroneous
allele rather than genotype. In other words, the calculation of the discordance
score now considers the probability of genotyping error to be different
for HOM and HET genotypes, i.e. P(0/1|dsg=0) > P(1/1|dsg=0).
- fixes in HWE score calculation plus output average HWE score rather
than absolute HWE score
- better description of fields
* bcftools merge
- Add `-m` modifiers to suppress the output of the unseen allele <*> or <NON_REF>
at variant sites (e.g. `-m both,*`) or all sites (e.g. `-m both,**`)
* bcftools mpileup
- Output MIN_DP rather than MinDP in gVCF mode
* bcftools norm
- Add the number of joined lines to the summary output, for example
Lines total/split/joined/realigned/skipped: 6/0/3/0/0
- Allow combining -m and -a with --old-rec-tag (#2020)
- Symbolic <DEL> alleles caused norm to expand REF to the full length of the deletion.
This was not intended and problematic for long deletions, the REF allele should list
one base only (#2029)
* bcftools query
- Add new `-N, --disable-automatic-newline` option for pre-1.18 query formatting behavior
when newline would not be added when missing
- Make the automatic addition of the newline character in a more predictable way and,
when missing, always put it at the end of the expression. In version 1.18 it could
be added at the end of the expression (for per-site expressions) or inside the square
brackets (for per-sample expressions). The new behavior is:
- if the formatting expression contains a newline character, do nothing
- if there is no newline character and -N, --disable-automatic-newline is given, do nothing
- if there is no newline character and -N is not given, insert newline at the end of the expression
See #1969 for details
- Add new `-F, --print-filtered` option to output a default string for samples that would otherwise
be filtered by `-i/-e` expressions.
- Include sample name in the output header with `-H` whenever it makes sense (#1992)
* bcftools +spit-vep
- Fix on the fly filtering involving numeric subfields, e.g. `-i 'MAX_AF<0.001'` (#2039)
- Interpret default column type names (--columns-types) as entire strings, rather than
substrings to avoid unexpected spurious matches (i.e. internally add ^ and $ to all
field names)
* bcftools +trio-dnm2
- Do not flag paternal genotyping errors as de novo mutations. Specifically, when father's
chrX genotype is 0/1 and mother's 0/0, 0/1 in the child will not be marked as DNM.
* bcftools view
- Add new `-A, --trim-unseen-allele` option to remove the unseen allele <*> or <NON_REF>
at variant sites (`-A`) or all sites (`-AA`)
## Release 1.18 (25th July 2023)
Changes affecting the whole of bcftools, or multiple commands:
* Support auto indexing during writing BCF and VCF.gz via new `--write-index` option
Changes affecting specific commands:
* bcftools annotate
- The `-m, --mark-sites` option can be now used to mark all sites without the
need to provide the `-a` file (#1861)
- Fix a bug where the `-m` function did not respect the `--min-overlap` option (#1869)
- Fix a bug when update of INFO/END results in assertion error (#1957)
* bcftools concat
- New option `--drop-genotypes`
* bcftools consensus
- Support higher-ploidy genotypes with `-H, --haplotype` (#1892)
- Allow `--mark-ins` and `--mark-snv` with a character, similarly to `--mark-del`
* bcftools convert
- Support for conversion from tab-delimited files (CHROM,POS,REF,ALT) to sites-only VCFs
* bcftools csq
- New `--unify-chr-names` option to automatically unify different chromosome
naming conventions in the input GFF, fasta and VCF files (e.g. "chrX" vs "X")
- More versatility in parsing various flavors of GFF
- A new `--dump-gff` option to help with debugging and investigating the internals
of hGFF parsing
- When printing consequences in nonsense mediated decay transcripts, include 'NMD_transcript'
in the consequence part of the annotation. This is to make filtering easier and analogous to
VEP annotations. For example the consequence annotation
3_prime_utr|PCGF3|ENST00000430644|NMD
is newly printed as
3_prime_utr&NMD_transcript|PCGF3|ENST00000430644|NMD
* bcftools gtcheck
- Add stats for the number of sites matched in the GT-vs-GT, GT-vs-PL, etc modes. This
information is important for interpretation of the discordance score, as only the
GT-vs-GT matching can be interpreted as the number of mismatching genotypes.
* bcftools +mendelian2
- Fix in command line argument parsing, the `-p` and `-P` options were not
functioning (#1906)
* bcftools merge
- New `-M, --missing-rules` option to control the behavior of merging of vector tags
to prevent mixtures of known and missing values in tags when desired
- Use values pertaining to the unknown allele (<*> or <NON_REF>) when available
to prevent mixtures of known and missing values (#1888)
- Revamped line matching code to fix problems in gVCF merging where split gVCF blocks
would not update genotypes (#1891, #1164).
* bcftool mpileup
- Fix a bug in --indels-v2.0 which caused an endless loop when CIGAR operator 'H' or 'P'
was encountered
* bcftools norm
- The `-m, --multiallelics +` mode now preserves phasing (#1893)
- Symbolic <DEL.*> alleles are now normalized too (#1919)
- New `-g, --gff-annot` option to right-align indels in forward transcripts to follow
HGVS 3'rule (#1929)
* bcftools query
- Force newline character in formatting expression when not given explicitly
- Fix `-H` header output in formatting expressions containing newlines
* bcftools reheader
- Make `-f, --fai` aware of long contigs not representable by 32-bit integer (#1959)
* bcftools +split-vep
- Prevent a segfault when `-i/-e` use a VEP subfield not included in `-f` or `-c` (#1877)
- New `-X, --keep-sites` option complementing the existing `-x, --drop-sites` options
- Force newline character in formatting expression when not given explicitly
- Fix a subtle ambiguity: identical rows must be returned when `-s` is applied regardless
of `-f` containing the `-a` VEP tag itself or not.
* bcftools stats
- Collect new VAF (variant allele frequency) statistics from FORMAT/AD field
- When counting transitions/transversions, consider also alternate het genotypes
* plot-vcfstats
- Add three new VAF plots
## Release 1.17 (21st February 2023)
Changes affecting the whole of bcftools, or multiple commands:
* The -i/-e filtering expressions
- Error checks were added to prevent incorrect use of vector arithmetics. For example,
when evaluating the sum of two vectors A and B, the resulting vector could contain
nonsense values when the input vectors were not of the same length. The fix introduces
the following logic:
- evaluate to C_i = A_i + B_i when length(A)==B(A) and set length(C)=length(A)
- evaluate to C_i = A_i + B_0 when length(B)=1 and set length(C)=length(A)
- evaluate to C_i = A_0 + B_i when length(A)=1 and set length(C)=length(B)
- throw an error when length(A)!=length(B) AND length(A)!=1 AND length(B)!=1
- Arrays in Number=R tags can be now subscripted by alleles found in FORMAT/GT. For example,
FORMAT/AD[GT] > 10 .. require support of more than 10 reads for each allele
FORMAT/AD[0:GT] > 10 .. same as above, but in the first sample
sSUM(FORMAT/AD[GT]) > 20 .. require total sample depth bigger than 20
* The commands `consensus -H` and `+split-vep -H`
- Drop unnecessary leading space in the first header column and newly print `#[1]columnName`
instead of the previous `# [1]columnName` (#1856)
Changes affecting specific commands:
* bcftools +allele-length
- Fix overflow for indels longer than 512bp and aggregate alleles equal or larger than
that in the same bin (#1837)
* bcftools annotate
- Support sample reordering of annotation file (#1785)
- Restore lost functionality of the --pair-logic option (#1808)
* bcftools call
- Fix a bug where too many alleles passed to `-C alleles` via `-T` caused memory
corruption (#1790)
- Fix a bug where indels constrained with `-C alleles -T` would sometimes be missed (#1706)
* bcftools consensus
- BREAKING CHANGE: the option `-I, --iupac-codes` newly outputs IUPAC codes based on FORMAT/GT
of all samples. The `-s, --samples` and `-S, --samples-file` options can be used to subset
samples. In order to ignore samples and consider only the REF and ALT columns (the original
behavior prior to 1.17), run with `-s -` (#1828)
* bcftools convert
- Make variantkey conversion work for sites without an ALT allele (#1806)
* bcftool csq
- Fix a bug where a MNV with multiple consequences (e.g. missense + stop_gained)
would report only the less severe one (#1810)
- GFF file parsing was made slightly more flexible, newly ids can be just 'XXX'
rather than, for example, 'gene:XXX'
- New gff2gff perl script to fix GFF formatting differences
* bcftools +fill-tags
- More of the available annotations are now added by the `-t all` option
* bcftools +fixref
- New INFO/FIXREF annotation
- New -m swap mode
* bcftools +mendelian
- The +mendelian plugin has been deprecated and replaced with +mendelian2. The
function of the plugin is the same but the command line options and the output
format has changed, and for this was introduced as a new plugin.
* bcftools mpileup
- Most of the annotations generated by mpileup are now optional via the
`-a, --annotate` option and add several new (mostly experimental) annotations.
- New option `--indels-2.0` for an EXPERIMENTAL indel calling model. This model aims
to address some known deficiencies of the current indel calling algorithm, specifically,
it uses diploid reference consensus sequence. Note that in the current version it
has the potential to increase sensitivity but at the cost of decreased specificity.
- Make the FS annotation (Fisher exact test strand bias) functional and remove it
from the default annotations
* bcftools norm
- New --multi-overlaps option allows setting overlapping alleles either to the
ref allele (the current default) or to a missing allele (#1764 and #1802)
- Fixed a bug in `-m -` which does not split missing FORMAT values correctly and
could lead to empty FORMAT fields such as `::` instead of the correct `:.:` (#1818)
- The `--atomize` option previously would not split complex indels such as C>GGG.
Newly these will be split into two records C>G and C>CGG (#1832)
* bcftools query
- Fix a rare bug where the printing of SAMPLE field with `query` was incorrectly
suppressed when the `-e` option contained a sample expression while the formatting
query did not. See #1783 for details.
* bcftools +setGT
- Add new `--new-gt X` option (#1800)
- Add new `--target-gt r:FLOAT` option to randomly select a proportion of genotypes (#1850)
- Fix a bug where `-t ./x` mode was advertised as selecting both phased and unphased
half-missing genotypes, but was in fact selecting only unphased genotypes (#1844)
* bcftools +split-vep
- New options `-g, --gene-list` and `--gene-list-fields` which allow to prioritize
consequences from a list of genes, or restrict output to the listed genes
- New `-H, --print-header` option to print the header with `-f`
- Work around a bug in the LOFTEE VEP plugin used to annotate gnomAD VCFs. There the
LoF_info subfield contains commas which, in general, makes it impossible to parse the
VEP subfields. The +split-vep plugin can now work with such files, replacing the offending
commas with slash (/) characters. See also https://github.com/Ensembl/ensembl-vep/issues/1351
- Newly the `-c, --columns` option can be omitted when a subfield is used in `-i/-e` filtering
expression. Note that `-c` may still have to be given when it is not possible to infer the
type of the subfield. Note that this is an experimental feature.
* bcftools stats
- The per-sample stats (PSC) would not be computed when `-i/-e` filtering options and
the `-s -` option were given but the expression did not include sample columns (1835)
* bcftools +tag2tag
- Revamp of the plugin to allow wider range of tag conversions, specifically all combinations
from FORMAT/GL,PL,GP to FORMAT/GL,PL,GP,GT
* bcftools +trio-dnm2
- New `-n, --strictly-novel` option to downplay alleles which violate Mendelian
inheritance but are not novel
- Allow to set the `--pn` and `--pns` options separately for SNVs and indels and make
the indel settings more strict by default
- Output missing FORMAT/VAF values in non-trio samples, rather than random nonsense values
* bcftools +variant-distance
- New option `-d, --direction` to choose the directionality: forward, reverse, nearest (the default)
or both (#1829)
## Release 1.16 (18th August 2022)
* New plugin `bcftools +variant-distance` to annotate records with distance to the
nearest variant (#1690)
Changes affecting the whole of bcftools, or multiple commands:
* The -i/-e filtering expressions
- Added support for querying of multiple filters, for example `-i 'FILTER="A;B"'`
can be used to select sites with two filters "A" and "B" set. See the documentation
for more examples.
- Added modulo arithmetic operator
Changes affecting specific commands:
* bcftools annotate
- A bug introduced in 1.14 caused that records with INFO/END annotation would
incorrectly trigger `-c ~INFO/END` mode of comparison even when not explicitly
requested, which would result in not transferring the annotation from a tab-delimited
file (#1733)
* bcftools merge
- New `-m snp-ins-del` switch to merge SNVs, insertions and deletions separately (#1704)
* bcftools mpileup
- New NMBZ annotation for Mann-Whitney U-z test on number of mismatches within
supporting reads
- Suppress the output of MQSBZ and FS annotations in absence of alternate allele
* bcftools +scatter
- Fix erroneous addition of duplicate PG lines
* bcftools +setGT
- Custom genotypes (e.g. `-n c:1/1`) now correctly override ploidy
## Release 1.15.1 (7th April 2022)
* bcftools annotate
- New `-H, --header-line` convenience option to pass a header line on command line,
this complements the existing `-h, --header-lines` option which requires a file
with header lines
* bcftools csq
- A list of consequence types supported by `bcftools csq` has been added to
the manual page. (#1671)
* bcftools +fill-tags
- Extend generalized functions so that FORMAT tags can be filled as well, for example:
bcftools +fill-tags in.bcf -o out.bcf -- -t 'FORMAT/DP:1=int(smpl_sum(FORMAT/AD))'
- Allow multiple custom functions in a single run. Previously the program would silently
go with the last one, assigning the same values to all (#1684)
* 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`. This
option now checks that the REF allele only includes the allowed characters
A, C, G, T and N. (#1668)
- Fix the loss of phasing in half-missing genotypes in variant atomization (#1689)
* 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 (#1687)
* bcftools +split-vep
- VEP fields with characters disallowed in VCF tag names by the specification (such as '-'
in 'M-CAP') couldn't be queried. This has been fixed, the program now sanitizes the field
names, replacing invalid characters with underscore (#1686)
## Release 1.15 (21st February 2022)
* New `bcftools head` subcommand for conveniently displaying the headers
of a VCF or BCF file. Without any options, this is equivalent to
`bcftools view --header-only --no-version` but more succinct and memorable.
* The `-T, --targets-file` option had the following bug originating in HTSlib code:
when an uncompressed file with multiple columns CHR,POS,REF was provided, the
REF would be interpreted as 0 gigabases (#1598)
Changes affecting specific commands:
* 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 to specify the minimum required
overlap of intersecting regions
- Allow to transfer ALT from VCF with or without replacement using
bcftools annotate -a annots.vcf.gz -c ALT file.vcf.gz
bcftools annotate -a annots.vcf.gz -c +ALT file.vcf.gz
* bcftools convert
- Revamp of `--gensample`, `--hapsample` and `--haplegendsample` family of options
which includes the following changes:
- New `--3N6` option to output/input the new version of the .gen file format,
see https://www.cog-genomics.org/plink/2.0/formats#gen
- Deprecate the `--chrom` option in favor of `--3N6`. A simple `cut` command
can be used to convert from the new 3*M+6 column format to the format printed
with `--chrom` (`cut -d' ' -f1,3-`).
- 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. The column
is autodetected for `--gensample2vcf`, can be the first or the second for
`--hapsample2vcf` (depending on whether the `--vcf-ids` option is given), must be
the first for `--haplegendsample2vcf`.
* 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 (#1635)
* bcftools +fixref
- The `-m id` option now works also for non-dbSNP ids, i.e. not just `rsINT`
- New `-m flip-all` mode for flipping all sites, including ambiguous A/T and C/G sites
* bcftools isec
- Prevent segfault on sites filtered with -i/-e in all files (#1632)
* bcftools mpileup
- More flexible read filtering using the options
--ls, --skip-all-set .. skip reads with all of the FLAG bits set
--ns, --skip-any-set .. skip reads with any of the FLAG bits set
--lu, --skip-all-unset .. skip reads with all of the FLAG bits unset
--nu, --skip-any-unset .. skip reads with any of the FLAG bits unset
The existing synonymous options will continue to function but their use
is discouraged
--rf, --incl-flags STR|INT Required flags: skip reads with mask bits unset
--ff, --excl-flags STR|INT Filter flags: skip reads with mask bits set
* bcftools query
- Make the `--samples` and `--samples-file` options work also in the `--list-samples`
mode. Add a new `--force-samples` option which enables proceeding even when some of
the requested samples are not present in the VCF (#1631)
* 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. This problem
affected only the use of `-e` logic, not the `-i` expressions (#1607)
* 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
## Release 1.14 (22nd October 2021)
Changes affecting the whole of bcftools, or multiple commands:
* New `--regions-overlap` and `--targets-overlap` options which address
a long-standing design problem with subsetting VCF files by region.
BCFtools recognize two sets of options, one for streaming (`-t/-T`) and
one for index-gumping (`-r/-R`). They behave differently, the first
includes only records with POS coordinate within the regions, the other
includes overlapping regions. The two new options allow to modify the
default behavior, see the man page for more details.
* The `--output-type` option can be used to override the default compression
level
Changes affecting specific commands:
* bcftools annotate
- when `--set-id` and `--remove` are combined, `--set-id` cannot use
tags deleted by `--remove`. This is now detected and the program
exists with an informative error message instead of segfaulting
(#1540)
- while non-symbolic variation are uniquely identified by POS,REF,ALT,
symbolic alleles starting at the same position were undistinguishable.
This prevented correct matching of records with the same positions and
variant type but different length given by INFO/END (samtools/htslib@60977f2).
When annotating froma VCF/BCF, the matching is done automatically. When
annotating from a tab-delimited text file, this feature can be invoked
by using `-c INFO/END`.
- add a new '.' modifier to control wheter missing values should be carried
over from a tab-delimited file or not. For example:
-c TAG .. adds TAG if the source value is not missing. If TAG
exists in the target file, it will be overwritten
-c .TAG .. adds TAG even if the source value is missing. This
can overwrite non-missing values with a missing value
and can create empty VCF fields (`TAG=.`)
* bcftools +check-ploidy
- by default missing genotypes are not used when determining ploidy.
With the new option `-m, --use-missing` it is possible to use the
information carried in the missing and half-missing genotypes
(e.g. ".", "./." or "./1")
* bcftools concat:
- new `--ligate-force` and `--ligate-warn` options for finer control
of `-l, --ligate` behavior in imperfect overlaps. The new default is
to throw an error when sites present in one chunk but absent in the
other are encountered. To drop such sites and proceed, use the new
`--ligate-warn` option (previously this was the default). To keep such
sites, use the new `--ligate-force` option (#1567).
* bcftools consensus:
- Apply mask even when the VCF has no notion about the chromosome. It
was possible to encounter this problem when `contig` lines were not
present in the VCF header and no variants were called on that chromosome
(#1592)
* bcftools +contrast:
- support for chunking within map/reduce framework allowing to collect
NASSOC counts even for empty case/control sample sets (#1566)
* bcftools csq:
- bug fix, compound indels were not recognised in some cases (#1536)
- compound variants were incorrectly marked as 'inframe' even when
stop codon would occur before the frame was restored (#1551)
- 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 (#1539)
- 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 (#1578)
- 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 (#1394)
* bcftools mpileup:
- new --indel-size option which allows increase of 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 (#1503)
- assign as many alternate alleles to genotypes at multiallelic sites
in the`-m +` mode, disregarding the phase. Previously the program
assumed to be executed as an inverse operation of `-m -`, but when
that was not the case, reference alleles would have been filled
instead of multiple alternate alleles (#1542)
* bcftools sort:
- increase accuracy of the --max-mem option limit, previously the limit
could be exceeded by more than 20% (#1576)
* bcftools +trio-dnm:
- new `--with-pAD` option to allow processing of VCFs without FORMAT/QS.
The existing `--ppl` option was changed to the analogous `--with-pPL`
* bcftools view:
- the functionality of the option --compression-level lost in 1.12
has been restored
## Release 1.13 (7th July 2021)
This release brings new options and significant changes in BAQ parametrization
in `bcftools mpileup`. The previous behavior can be triggered by providing
the `--config 1.12` option. Please see https://github.com/samtools/bcftools/pull/1474
for details.
Changes affecting the whole of bcftools, or multiple commands:
* Improved build system
Changes affecting specific commands:
* 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. Then the
removed INFO/END continues to inform the end coordinate and causes
incorrect retrieval of records with the -r option (#1483)
- Support for matching annotation line by ID, in addition to CHROM,POS,REF,
and ALT (#1461)
bcftools annotate -a annots.tab.gz -c CHROM,POS,~ID,REF,ALT,INFO/END input.vcf
* bcftools csq:
- When GFF and VCF/fasta use a different chromosome naming convention
(e.g. chrX vs X), no consequences would be added. Newly the program
attempts to detect these differences and remove/add the "chr" prefix
to chromosome name to match the GFF and VCF/fasta (#1507)
- Parametrize brief-predictions parameter to allow explicit number of
aminoacids to be printed. Note that the `-b, --brief-predictions` option
is being replaced with `-B, --trim-protein-seq INT`
* bcftools +fill-tags:
- Generalization and better support for custom functions that allow
adding new INFO tags based on arbitrary `-i, --include` type of
expressions. For example, to calculate a missing INFO/DP annotation
from FORMAT/AD, it is possible to use:
-t 'DP:1=int(sum(FORMAT/AD))'
Here the optional ":1" part specifies that a single value will be
added (by default Number=. is used) and the optional int(...) adds
an integer value (by default Type=Float is used).
- 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 (#1444)
- Minor bug fix, with PLs being the default, the `--distinctive-sites` option
started to require explicit `--error-probability 0`
* bcftools index:
- The program now accepts both data file name and the index file name. This
adds to user convenience when running index statistics (-n, -s)
* bcftools isec:
- Always generate sites.txt with isec -p (#1462)
* bcftools +mendelian:
- Consider only complete trios, do not crash on sample name typos (#1520)
* 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. Previously
only reads with indels were included at indel sites.
- Major revamp of BAQ. Please see https://github.com/samtools/bcftools/pull/1474
for details. The previous behavior can be triggered by providing the `--config 1.12`
option.
- Thanks to improvements in HTSlib, the removal of overlapping reads (which can
be disabled with the `-x, --ignore-overlaps` options) is not systematically biased
anymore (https://github.com/samtools/htslib/pull/1273)
- Modified scale of Mann-Whitney U tests. Newly INFO/*Z annotations will be printed,
for example MQBZ replaces MQB.
* bcftools norm:
- Fix Type=Flag output in `norm --atomize` (#1472)
- 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. For example, to force a heterozygous
genotype it is now possible to use expressions like:
c:'m|M'
c:0/1
c:0
* bcftools +split-vep:
- New `-u, --allow-undef-tags` option
- Better handling of ambiguous keys such as INFO/AF and CSQ/AD. The
`-p, --annot-prefix` option is now applied before doing anything else
which allows its use with `-f, --format` and `-c, --columns` options.
- Some consequence field names may not constitute a valid tag name, such
as "pos(1-based)". Newly field names are trimmed to exclude brackets.
* bcftools +tag2tag:
- New --QR-QA-to-QS option to convert annotations generated by Freebays
to QS used by BCFtools
* bcftools +trio-dnm:
- Add support for sites with more than four alleles. Note that only the
four most frequent alleles are considered, the model remains unchanged.
Previously such sites were skipped.
- New --use-NAIVE option for a naive DNM calling based solely on FORMAT/GT
and expected Mendelian inheritance. This option is suitable for prefiltering.
- Fix behavior 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 trehsholds independently
## Release 1.12 (17th March 2021)
Changes affecting the whole of bcftools, or multiple commands:
* 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 (#1343)
* 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. For
example, the new behavior could be:
bcftools query -f'[%POS %SAMPLE %GT\n]' -i'N_PASS(GT="alt")==1'
11 A 0/0
11 B 0/0
11 C 1/1
while previously the same expression would return:
11 C 1/1
The original mode can be mimicked by splitting the filtering into two steps:
bcftools view -i'N_PASS(GT="alt")==1' | \
bcftools query -f'[%POS %SAMPLE %GT\n]' -i'GT="alt"'
Changes affecting specific commands:
* bcftools annotate:
- New `--rename-annots` option to help fix broken VCFs (#1335)
- New -C option allows a long list of options to be read 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. Note that this is
not bullet proof. In order for this to work:
- the annotation file must have one line per ALT allele
- fields must contain a single value as multiple values are appended
as they are and would break the correspondence between the alleles