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// bcftools.txt -- asciidoc template for the bcftools man page and html.
//
// Please do not modify bcftools.1 or bcftools.html directly,
// edit this file and convert using the following commands:
//
// make docs
//
// or
//
// a2x --doctype manpage --format manpage bcftools.txt
// a2x --doctype manpage --format xhtml bcftools.txt
//
// Contributions are welcome, simply edit this file and send
// a pull request or email the modified file directly.
//
bcftools(1)
===========
:doctype: manpage
NAME
----
bcftools - utilities for variant calling and manipulating VCFs and BCFs.
SYNOPSIS
--------
*bcftools* [--version|--version-only] [--help] ['COMMAND'] ['OPTIONS']
DESCRIPTION
-----------
BCFtools is a set of utilities that manipulate variant calls in the Variant
Call Format (VCF) and its binary counterpart BCF. All commands work
transparently with both VCFs and BCFs, both uncompressed and BGZF-compressed.
Most commands accept VCF, bgzipped VCF and BCF with filetype detected
automatically even when streaming from a pipe. Indexed VCF and BCF
will work in all situations. Un-indexed VCF and BCF and streams will
work in most, but not all situations. In general, whenever multiple VCFs are
read simultaneously, they must be indexed and therefore also compressed.
(Note that files with non-standard index names can be accessed as e.g.
"`bcftools view -r X:2928329 file.vcf.gz##idx##non-standard-index-name`".)
BCFtools is designed to work on a stream. It regards an input file "-" as the
standard input (stdin) and outputs to the standard output (stdout). Several
commands can thus be combined with Unix pipes.
=== VERSION
This manual page was last updated *{date}* and refers to bcftools git version *{version}*.
=== BCF1
The BCF1 format output by versions of samtools \<= 0.1.19 is *not*
compatible with this version of bcftools. To read BCF1 files one can use
the view command from old versions of bcftools packaged with samtools
versions \<= 0.1.19 to convert to VCF, which can then be read by
this version of bcftools.
----
samtools-0.1.19/bcftools/bcftools view file.bcf1 | bcftools view
----
=== VARIANT CALLING
See 'bcftools call' for variant calling from the output of the
'samtools mpileup' command. In versions of samtools \<= 0.1.19 calling was
done with 'bcftools view'. Users are now required to choose between the old
samtools calling model ('-c/--consensus-caller') and the new multiallelic
calling model ('-m/--multiallelic-caller'). The multiallelic calling model
is recommended for most tasks.
LIST OF COMMANDS
----------------
For a full list of available commands, run *bcftools* without arguments. For a full
list of available options, run *bcftools* 'COMMAND' without arguments.
- *<<annotate,annotate>>* .. edit VCF files, add or remove annotations
- *<<call,call>>* .. SNP/indel calling (former "view")
- *<<cnv,cnv>>* .. Copy Number Variation caller
- *<<concat,concat>>* .. concatenate VCF/BCF files from the same set of samples
- *<<consensus,consensus>>* .. create consensus sequence by applying VCF variants
- *<<convert,convert>>* .. convert VCF/BCF to other formats and back
- *<<csq,csq>>* .. haplotype aware consequence caller
- *<<filter,filter>>* .. filter VCF/BCF files using fixed thresholds
- *<<gtcheck,gtcheck>>* .. check sample concordance, detect sample swaps and contamination
- *<<index,index>>* .. index VCF/BCF
- *<<isec,isec>>* .. intersections of VCF/BCF files
- *<<merge,merge>>* .. merge VCF/BCF files files from non-overlapping sample sets
- *<<mpileup,mpileup>>* .. multi-way pileup producing genotype likelihoods
- *<<norm,norm>>* .. normalize indels
- *<<plugin,plugin>>* .. run user-defined plugin
- *<<polysomy,polysomy>>* .. detect contaminations and whole-chromosome aberrations
- *<<query,query>>* .. transform VCF/BCF into user-defined formats
- *<<reheader,reheader>>* .. modify VCF/BCF header, change sample names
- *<<roh,roh>>* .. identify runs of homo/auto-zygosity
- *<<sort,sort>>* .. sort VCF/BCF files
- *<<stats,stats>>* .. produce VCF/BCF stats (former vcfcheck)
- *<<view,view>>* .. subset, filter and convert VCF and BCF files
LIST OF SCRIPTS
---------------
Some helper scripts are bundled with the bcftools code.
- *<<plot-vcfstats,plot-vcfstats>>* .. plots the output of *<<stats,stats>>*
COMMANDS AND OPTIONS
--------------------
[[common_options]]
=== Common Options
The following options are common to many bcftools commands. See usage for
specific commands to see if they apply.
'FILE'::
Files can be both VCF or BCF, uncompressed or BGZF-compressed. The file "-"
is interpreted as standard input. Some tools may require tabix- or
CSI-indexed files.
*-c, --collapse* 'snps'|'indels'|'both'|'all'|'some'|'none'|'id'::
Controls how to treat records with duplicate positions and defines compatible
records across multiple input files. Here by "compatible" we mean records which
should be considered as identical by the tools. For example, when performing
line intersections, the desire may be to consider as identical all sites with
matching positions (*bcftools isec -c* 'all'), or only sites with matching variant
type (*bcftools isec -c* 'snps'{nbsp} *-c* 'indels'), or only sites with all alleles
identical (*bcftools isec -c* 'none').
'none';;
only records with identical REF and ALT alleles are compatible
'some';;
only records where some subset of ALT alleles match are compatible
'all';;
all records are compatible, regardless of whether the ALT alleles
match or not. In the case of records with the same position, only
the first will be considered and appear on output.
'snps';;
any SNP records are compatible, regardless of whether the ALT
alleles match or not. For duplicate positions, only the first SNP
record will be considered and appear on output.
'indels';;
all indel records are compatible, regardless of whether the REF
and ALT alleles match or not. For duplicate positions, only the
first indel record will be considered and appear on output.
'both';;
abbreviation of "*-c* 'indels'{nbsp} *-c* 'snps'"
'id';;
only records with identical ID column are compatible.
Supported by *<<merge,bcftools merge>>* only.
*-f, --apply-filters* 'LIST'::
Skip sites where FILTER column does not contain any of the strings listed
in 'LIST'. For example, to include only sites which have no filters set,
use *-f* '.,PASS'.
*--no-version*::
Do not append version and command line information to the output VCF header.
*-o, --output* 'FILE'::
When output consists of a single stream, write it to 'FILE' rather than
to standard output, where it is written by default.
*-O, --output-type* 'b'|'u'|'z'|'v'::
Output compressed BCF ('b'), uncompressed BCF ('u'), compressed VCF ('z'), uncompressed VCF ('v').
Use the -Ou option when piping between bcftools subcommands to speed up
performance by removing unnecessary compression/decompression and
VCF<-->BCF conversion.
*-r, --regions* 'chr'|'chr:pos'|'chr:beg-end'|'chr:beg-'[,...]::
Comma-separated list of regions, see also *-R, --regions-file*. Overlapping
records are matched even when the starting coordinate is outside of the
region, unlike the *-t/-T* options where only the POS coordinate is checked.
Note that *-r* cannot be used in combination with *-R*.
*-R, --regions-file* 'FILE'::
Regions can be specified either on command line or in a VCF, BED, or
tab-delimited file (the default). The columns of the tab-delimited file
can contain either positions (two-column format) or intervals (three-column
format): CHROM, POS, and, optionally, END, where positions are 1-based
and inclusive. The columns of the tab-delimited BED file are also
CHROM, POS and END (trailing columns are ignored), but coordinates
are 0-based, half-open. To indicate that a file be treated as BED rather
than the 1-based tab-delimited file, the file must have the ".bed" or
".bed.gz" suffix (case-insensitive). Uncompressed files are stored in
memory, while bgzip-compressed and tabix-indexed region files are streamed.
Note that sequence names must match exactly, "chr20" is not the same as
"20". Also note that chromosome ordering in 'FILE' will be respected,
the VCF will be processed in the order in which chromosomes first appear
in 'FILE'. However, within chromosomes, the VCF will always be
processed in ascending genomic coordinate order no matter what order they
appear in 'FILE'. Note that overlapping regions in 'FILE' can result in
duplicated out of order positions in the output.
This option requires indexed VCF/BCF files. Note that *-R* cannot be used
in combination with *-r*.
*--regions-overlap* '0'|'1'|'2'::
This option controls how overlapping records are determined:
set to *0* if the VCF record has to have POS inside a region
(this corresponds to the default behavior of *-t/-T*);
set to *1* if also overlapping records with POS outside a region
should be included (this is the default behavior of *-r/-R*); or set
to *2* to include only true overlapping variation (compare
the full VCF representation "`TA>T-`" vs the true sequence variation "`A>-`").
*-s, --samples* \[^]'LIST'::
Comma-separated list of samples to include or exclude if prefixed
with "^".
The sample order is updated to reflect that given on the command line.
Note that in general tags such as INFO/AC, INFO/AN, etc are not updated
to correspond to the subset samples. *<<view,bcftools view>>* is the
exception where some tags will be updated (unless the *-I, --no-update*
option is used; see *<<view,bcftools view>>* documentation). To use updated
tags for the subset in another command one can pipe from *view* into
that command. For example:
----
bcftools view -Ou -s sample1,sample2 file.vcf | bcftools query -f %INFO/AC\t%INFO/AN\n
----
*-S, --samples-file* [^]'FILE'[[samples_file]]::
File of sample names to include or exclude if prefixed with "^".
One sample per line. See also the note above for the *-s, --samples*
option.
The sample order is updated to reflect that given in the input file.
The command *<<call,bcftools call>>* accepts an optional second
column indicating ploidy (0, 1 or 2) or sex (as defined by
*<<ploidy,--ploidy>>*, for example "F" or "M"), for example:
----
sample1 1
sample2 2
sample3 2
----
or
----
sample1 M
sample2 F
sample3 F
----
If the second column is not present, the sex "F" is assumed.
With *<<call,bcftools call>> -C* 'trio', PED file is expected.
The program ignores the first column and the last indicates sex (1=male, 2=female), for example:
----
ignored_column daughterA fatherA motherA 2
ignored_column sonB fatherB motherB 1
----
*-t, --targets* \[^]'chr'|'chr:pos'|'chr:from-to'|'chr:from-'[,...]::
Similar as *-r, --regions*, but the next position is accessed by streaming the
whole VCF/BCF rather than using the tbi/csi index. Both *-r* and *-t* options
can be applied simultaneously: *-r* uses the index to jump to a region
and *-t* discards positions which are not in the targets. Unlike *-r*, targets
can be prefixed with "^" to request logical complement. For example, "^X,Y,MT"
indicates that sequences X, Y and MT should be skipped.
Yet another difference between the *-t/-T* and *-r/-R* is that *-r/-R* checks for
proper overlaps and considers both POS and the end position of an indel, while *-t/-T*
considers the POS coordinate only. Note that *-t* cannot be used in combination with *-T*.
*-T, --targets-file* \[^]'FILE'::
Same *-t, --targets*, but reads regions from a file. Note that *-T*
cannot be used in combination with *-t*.
+
With the *call -C* 'alleles' command, third column of the targets file must
be comma-separated list of alleles, starting with the reference allele.
Note that the file must be compressed and indexed.
Such a file can be easily created from a VCF using:
----
bcftools query -f'%CHROM\t%POS\t%REF,%ALT\n' file.vcf | bgzip -c > als.tsv.gz && tabix -s1 -b2 -e2 als.tsv.gz
----
*--targets-overlap* '0'|'1'|'2'::
Same as *--regions-overlap* but for *-t/-T*.
*--threads* 'INT'::
Use multithreading with 'INT' worker threads. The option is currently used only for the compression of the
output stream, only when '--output-type' is 'b' or 'z'. Default: 0.
[[annotate]]
=== bcftools annotate '[OPTIONS]' 'FILE'
Add or remove annotations.
*-a, --annotations* 'file'::
Bgzip-compressed and tabix-indexed file with annotations. The file
can be VCF, BED, or a tab-delimited file with mandatory columns CHROM, POS
(or, alternatively, FROM and TO), optional columns REF and ALT, and arbitrary
number of annotation columns. BED files are expected to have
the ".bed" or ".bed.gz" suffix (case-insensitive), otherwise a tab-delimited file is assumed.
Note that in case of tab-delimited file, the coordinates POS, FROM and TO are
one-based and inclusive. When REF and ALT are present, only matching VCF
records will be annotated. If the END coordinate is present in the annotation file
and given on command line as "`-c ~INFO/END`", then VCF records will be matched also by the INFO/END coordinate.
If ID is present in the annotation file and given as "`-c ~ID`", then VCF records will be matched
also by the ID column.
{nbsp} +
{nbsp} +
When multiple ALT alleles are present in the annotation file (given as
comma-separated list of alleles), at least one must match one of the
alleles in the corresponding VCF record. Similarly, at least one
alternate allele from a multi-allelic VCF record must be present in the
annotation file.
{nbsp} +
{nbsp} +
Missing values can be added by providing "." in place of actual value
and using the missing value modifier with *-c*, such as ".TAG".
{nbsp} +
{nbsp} +
Note that flag types, such as "INFO/FLAG", can be annotated by including
a field with the value "1" to set the flag, "0" to remove it, or "." to
keep existing flags.
See also *-c, --columns* and *-h, --header-lines*.
----
# Sample annotation file with columns CHROM, POS, STRING_TAG, NUMERIC_TAG
1 752566 SomeString 5
1 798959 SomeOtherString 6
----
*--collapse* 'snps'|'indels'|'both'|'all'|'some'|'none'::
Controls how to match records from the annotation file to the target VCF.
Effective only when *-a* is a VCF or BCF.
See *<<common_options,Common Options>>* for more.
*-c, --columns* 'list'::
Comma-separated list of columns or tags to carry over from the annotation file
(see also *-a, --annotations*). If the annotation file is not a VCF/BCF,
'list' describes the columns of the annotation file and must include CHROM,
POS (or, alternatively, FROM and TO), and optionally REF and ALT. Unused
columns which should be ignored can be indicated by "-".
{nbsp} +
{nbsp} +
If the annotation file is a VCF/BCF, only the edited columns/tags must be present and their
order does not matter. The columns ID, QUAL, FILTER, INFO and FORMAT
can be edited, where INFO tags can be written both as "INFO/TAG" or simply "TAG",
and FORMAT tags can be written as "FORMAT/TAG" or "FMT/TAG".
The imported VCF annotations can be renamed as "DST_TAG:=SRC_TAG" or "FMT/DST_TAG:=FMT/SRC_TAG".
{nbsp} +
{nbsp} +
To carry over all INFO annotations, use "INFO". To add all INFO annotations except
"TAG", use "^INFO/TAG". By default, existing values are replaced.
{nbsp} +
{nbsp} +
By default, existing tags are overwritten unless the source value is a missing value (i.e. ".").
If also missing values should be carried over (and overwrite existing tags), use ".TAG" instead of "TAG".
To add annotations without overwriting existing values (that is, to add tags that are absent or
to add values to existing tags with missing values), use "+TAG" instead of "TAG". These can be combined,
for example ".+TAG" can be used to add TAG even if the source value is missing but only if TAG does not
exist in the target file; existing tags will not be overwritten.
To append to existing values (rather than replacing or leaving untouched), use "=TAG"
(instead of "TAG" or "+TAG").
To replace only existing values without modifying missing annotations, use "-TAG".
To match the record also by ID or INFO/END, in addition to REF and ALT, use "~ID" or "~INFO/END".
If position needs to be replaced, mark the column with the new position as "~POS".
{nbsp} +
{nbsp} +
If the annotation file is not a VCF/BCF, all new annotations must be
defined via *-h, --header-lines*.
{nbsp} +
{nbsp} +
See also the *-l, --merge-logic* option.
*-C, --columns-file* 'file'::
Read the list of columns from a file (normally given via the *-c, --columns* option).
"-" to skip a column of the annotation file.
One column name per row, an additional space- or tab-separated field can
be present to indicate the merge logic (normally given via the *-l, --merge-logic* option).
This is useful when many annotations are added at once.
*-e, --exclude* 'EXPRESSION'::
exclude sites for which 'EXPRESSION' is true. For valid expressions see
*<<expressions,EXPRESSIONS>>*.
*--force*::
continue even when parsing errors, such as undefined tags, are encountered. Note
this can be an unsafe operation and can result in corrupted BCF files. If this
option is used, make sure to sanity check the result thoroughly.
*-h, --header-lines* 'file'::
Lines to append to the VCF header, see also *-c, --columns* and *-a, --annotations*. For example:
----
##INFO=<ID=NUMERIC_TAG,Number=1,Type=Integer,Description="Example header line">
##INFO=<ID=STRING_TAG,Number=1,Type=String,Description="Yet another header line">
----
*-I, --set-id* \[+]'FORMAT'::
assign ID on the fly. The format is the same as in the *<<query,query>>*
command (see below). By default all existing IDs are replaced. If the
format string is preceded by "+", only missing IDs will be set. For example,
one can use
----
bcftools annotate --set-id +'%CHROM\_%POS\_%REF\_%FIRST_ALT' file.vcf
----
*-i, --include* 'EXPRESSION'::
include only sites for which 'EXPRESSION' is true. For valid expressions see
*<<expressions,EXPRESSIONS>>*.
*-k, --keep-sites*::
keep sites which do not pass *-i* and *-e* expressions instead of discarding them
*-l, --merge-logic* 'tag:first'|'append'|'append-missing'|'unique'|'sum'|'avg'|'min'|'max'[,...]::
When multiple regions overlap a single record, this option defines how to treat multiple
annotation values when setting 'tag' in the destination file: use the first encountered value ignoring
the rest ('first'); append allowing duplicates ('append'); append even if the appended value is missing,
i.e. is a dot ('append-missing'); append discarding duplicate values ('unique');
sum the values ('sum', numeric fields only); average the values ('avg'); use the minimum value ('min') or
the maximum ('max').
+
Note that this option is intended for use with BED or TAB-delimited annotation files only. Moreover,
it is effective only when either 'REF' and 'ALT' or 'BEG' and 'END' *--columns* are present .
+
Multiple rules can be given either as a comma-separated list or giving the option multiple times.
This is an experimental feature.
*-m, --mark-sites* [+-]'TAG'::
annotate sites which are present ("+") or absent ("-") in the *-a* file with a new INFO/TAG flag
*--no-version*::
see *<<common_options,Common Options>>*
*-o, --output* 'FILE'::
see *<<common_options,Common Options>>*
*-O, --output-type* 'b'|'u'|'z'|'v'::
see *<<common_options,Common Options>>*
*-r, --regions* 'chr'|'chr:pos'|'chr:from-to'|'chr:from-'[,...]::
see *<<common_options,Common Options>>*
*-R, --regions-file* 'file'::
see *<<common_options,Common Options>>*
*--rename-annots* 'file'::
rename annotations according to the map in 'file', with
"old_name new_name\n" pairs separated by whitespaces, each on a separate
line. The old name must be prefixed with the annotation type:
INFO, FORMAT, or FILTER.
*--rename-chrs* 'file'::
rename chromosomes according to the map in 'file', with
"old_name new_name\n" pairs separated by whitespaces, each on a separate
line.
*-s, --samples* \[^]'LIST'::
subset of samples to annotate, see also *<<common_options,Common Options>>*
*-S, --samples-file* 'FILE'::
subset of samples to annotate. If the samples are named differently in the
target VCF and the *-a, --annotations* VCF, the name mapping can be
given as "src_name dst_name\n", separated by whitespaces, each pair on a
separate line.
*--single-overlaps*::
use this option to keep memory requirements low with very large annotation
files. Note, however, that this comes at a cost, only single overlapping intervals
are considered in this mode. This was the default mode until the commit
af6f0c9 (Feb 24 2019).
*--threads* 'INT'::
see *<<common_options,Common Options>>*
*-x, --remove* 'list'::
List of annotations to remove. Use "FILTER" to remove all filters or
"FILTER/SomeFilter" to remove a specific filter. Similarly, "INFO" can
be used to remove all INFO tags and "FORMAT" to remove all FORMAT tags
except GT. To remove all INFO tags except "FOO" and "BAR", use
"^INFO/FOO,INFO/BAR" (and similarly for FORMAT and FILTER).
"INFO" can be abbreviated to "INF" and "FORMAT" to "FMT".
*Examples:*
----
# Remove three fields
bcftools annotate -x ID,INFO/DP,FORMAT/DP file.vcf.gz
# Remove all INFO fields and all FORMAT fields except for GT and PL
bcftools annotate -x INFO,^FORMAT/GT,FORMAT/PL file.vcf
# Add ID, QUAL and INFO/TAG, not replacing TAG if already present
bcftools annotate -a src.bcf -c ID,QUAL,+TAG dst.bcf
# Carry over all INFO and FORMAT annotations except FORMAT/GT
bcftools annotate -a src.bcf -c INFO,^FORMAT/GT dst.bcf
# Annotate from a tab-delimited file with six columns (the fifth is ignored),
# first indexing with tabix. The coordinates are 1-based.
tabix -s1 -b2 -e2 annots.tab.gz
bcftools annotate -a annots.tab.gz -h annots.hdr -c CHROM,POS,REF,ALT,-,TAG file.vcf
# Annotate from a tab-delimited file with regions (1-based coordinates, inclusive)
tabix -s1 -b2 -e3 annots.tab.gz
bcftools annotate -a annots.tab.gz -h annots.hdr -c CHROM,FROM,TO,TAG input.vcf
# Annotate from a bed file (0-based coordinates, half-closed, half-open intervals)
bcftools annotate -a annots.bed.gz -h annots.hdr -c CHROM,FROM,TO,TAG input.vcf
# Transfer the INFO/END tag, matching by POS,REF,ALT and ID. This example assumes
# that INFO/END is already present in the VCF header.
bcftools annotate -a annots.tab.gz -c CHROM,POS,~ID,REF,ALT,INFO/END input.vcf
# For more examples see http://samtools.github.io/bcftools/howtos/annotate.html
----
[[call]]
=== bcftools call '[OPTIONS]' 'FILE'
This command replaces the former *bcftools view* caller. Some of the original
functionality has been temporarily lost in the process of transition under
http://github.com/samtools/htslib[htslib], but will be added back on popular
demand. The original calling model can be invoked with the *-c* option.
==== File format options:
*--no-version*::
see *<<common_options,Common Options>>*
*-o, --output* 'FILE'::
see *<<common_options,Common Options>>*
*-O, --output-type* 'b'|'u'|'z'|'v'::
see *<<common_options,Common Options>>*
*--ploidy* 'ASSEMBLY'['?'][[ploidy]]::
predefined ploidy, use 'list' (or any other unused word) to print a list
of all predefined assemblies. Append a question mark to print the actual
definition. See also *--ploidy-file*.
*--ploidy-file* 'FILE'::
ploidy definition given as a space/tab-delimited list of
CHROM, FROM, TO, SEX, PLOIDY. The SEX codes are arbitrary and
correspond to the ones used by *<<samples_file,--samples-file>>*.
The default ploidy can be given using the starred records (see
below), unlisted regions have ploidy 2. The default ploidy definition is
----
X 1 60000 M 1
X 2699521 154931043 M 1
Y 1 59373566 M 1
Y 1 59373566 F 0
MT 1 16569 M 1
MT 1 16569 F 1
* * * M 2
* * * F 2
----
*-r, --regions* 'chr'|'chr:pos'|'chr:from-to'|'chr:from-'[,...]::
see *<<common_options,Common Options>>*
*-R, --regions-file* 'file'::
see *<<common_options,Common Options>>*
*-s, --samples* 'LIST'::
see *<<common_options,Common Options>>*
*-S, --samples-file* 'FILE'::
see *<<common_options,Common Options>>*
*-t, --targets* 'LIST'::
see *<<common_options,Common Options>>*
*-T, --targets-file* 'FILE'::
see *<<common_options,Common Options>>*
*--threads* 'INT'::
see *<<common_options,Common Options>>*
==== Input/output options:
*-A, --keep-alts*::
output all alternate alleles present in the alignments even if they do not
appear in any of the genotypes
*-f, --format-fields* 'list'::
comma-separated list of FORMAT fields to output for each sample. Currently
GQ and GP fields are supported. For convenience, the fields can be given
as lower case letters. Prefixed with "^" indicates a request for tag
removal of auxiliary tags useful only for calling.
*-F, --prior-freqs* 'AN','AC'::
take advantage of prior knowledge of population allele frequencies. The
workflow looks like this:
----
# Extract AN,AC values from an existing VCF, such 1000Genomes
bcftools query -f'%CHROM\t%POS\t%REF\t%ALT\t%AN\t%AC\n' 1000Genomes.bcf | bgzip -c > AFs.tab.gz
# If the tags AN,AC are not already present, use the +fill-tags plugin
bcftools +fill-tags 1000Genomes.bcf | bcftools query -f'%CHROM\t%POS\t%REF\t%ALT\t%AN\t%AC\n' | bgzip -c > AFs.tab.gz
tabix -s1 -b2 -e2 AFs.tab.gz
# Create a VCF header description, here we name the tags REF_AN,REF_AC
cat AFs.hdr
##INFO=<ID=REF_AN,Number=1,Type=Integer,Description="Total number of alleles in reference genotypes">
##INFO=<ID=REF_AC,Number=A,Type=Integer,Description="Allele count in reference genotypes for each ALT allele">
# Now before calling, stream the raw mpileup output through `bcftools annotate` to add the frequencies
bcftools mpileup [...] -Ou | bcftools annotate -a AFs.tab.gz -h AFs.hdr -c CHROM,POS,REF,ALT,REF_AN,REF_AC -Ou | bcftools call -mv -F REF_AN,REF_AC [...]
----
*-G, --group-samples* [TAG:]'FILE'|'-'::
by default, all samples are assumed to come from a single population. This option allows to group samples
into populations and apply the HWE assumption within but not across the populations. 'FILE' is a tab-delimited
text file with sample names in the first column and group names in the second column. If '-' is
given instead, no HWE assumption is made at all and single-sample calling is performed. (Note that
in low coverage data this inflates the rate of false positives.) The *-G* option requires the presence of
per-sample FORMAT/QS or FORMAT/AD tag generated with *bcftools mpileup -a QS* (or *-a AD*).
*-g, --gvcf* 'INT'::
output also gVCF blocks of homozygous REF calls. The parameter 'INT' is the
minimum per-sample depth required to include a site in the non-variant
block.
*-i, --insert-missed* 'INT'::
output also sites missed by mpileup but present in *-T, --targets-file*.
*-M, --keep-masked-ref*::
output sites where REF allele is N
*-V, --skip-variants* 'snps'|'indels'::
skip indel/SNP sites
*-v, --variants-only*::
output variant sites only
==== Consensus/variant calling options:
*-c, --consensus-caller*::
the original *samtools*/*bcftools* calling method (conflicts with *-m*)
*-C, --constrain* 'alleles'|'trio'::
'alleles';;
call genotypes given alleles. See also *-T, --targets-file*.
'trio';;
call genotypes given the father-mother-child constraint. See also
*-s, --samples* and *-n, --novel-rate*.
*-m, --multiallelic-caller*::
alternative model for multiallelic and rare-variant calling designed to
overcome known limitations in *-c* calling model (conflicts with *-c*)
*-n, --novel-rate* 'float'[,...]::
likelihood of novel mutation for constrained *-C* 'trio' calling. The trio
genotype calling maximizes likelihood of a particular combination of
genotypes for father, mother and the child
P(F=i,M=j,C=k) = P(unconstrained) * Pn + P(constrained) * (1-Pn).
By providing three values, the mutation rate Pn is set explicitly for SNPs,
deletions and insertions, respectively. If two values are given, the first
is interpreted as the mutation rate of SNPs and the second is used to
calculate the mutation rate of indels according to their length as
Pn='float'*exp(-a-b*len), where a=22.8689, b=0.2994 for insertions and
a=21.9313, b=0.2856 for deletions [pubmed:23975140]. If only one value is
given, the same mutation rate Pn is used for SNPs and indels.
*-p, --pval-threshold* 'float'::
with *-c*, accept variant if P(ref|D) < 'float'.
*-P, --prior* 'float'::
expected substitution rate, or 0 to disable the prior. Only with *-m*.
*-t, --targets* 'file'|'chr'|'chr:pos'|'chr:from-to'|'chr:from-'[,...]::
see *<<common_options,Common Options>>*
*-X, --chromosome-X*::
haploid output for male samples (requires PED file with *-s*)
*-Y, --chromosome-Y*::
haploid output for males and skips females (requires PED file with *-s*)
[[cnv]]
=== bcftools cnv '[OPTIONS]' 'FILE'
Copy number variation caller, requires a VCF annotated with the Illumina's
B-allele frequency (BAF) and Log R Ratio intensity (LRR) values. The HMM
considers the following copy number states: CN 2 (normal), 1 (single-copy
loss), 0 (complete loss), 3 (single-copy gain).
==== General Options:
*-c, --control-sample* 'string'::
optional control sample name. If given, pairwise calling is performed
and the *-P* option can be used
*-f, --AF-file* 'file'::
read allele frequencies from a tab-delimited file with the columns CHR,POS,REF,ALT,AF
*-o, --output-dir* 'path'::
output directory
*-p, --plot-threshold* 'float'::
call *matplotlib* to produce plots for chromosomes with quality at least 'float',
useful for visual inspection of the calls. With *-p 0*, plots for all chromosomes will be
generated. If not given, a *matplotlib* script will be created but not called.
*-r, --regions* 'chr'|'chr:pos'|'chr:from-to'|'chr:from-'[,...]::
see *<<common_options,Common Options>>*
*-R, --regions-file* 'file'::
see *<<common_options,Common Options>>*
*-s, --query-sample* 'string'::
query sample name
*-t, --targets* 'LIST'::
see *<<common_options,Common Options>>*
*-T, --targets-file* 'FILE'::
see *<<common_options,Common Options>>*
==== HMM Options:
*-a, --aberrant* 'float'[,'float']::
fraction of aberrant cells in query and control. The hallmark of
duplications and contaminations is the BAF value of heterozygous markers
which is dependent on the fraction of aberrant cells. Sensitivity to
smaller fractions of cells can be increased by setting *-a* to a lower value. Note
however, that this comes at the cost of increased false discovery rate.
*-b, --BAF-weight* 'float'::
relative contribution from BAF
*-d, --BAF-dev* 'float'[,'float']::
expected BAF deviation in query and control, i.e. the noise observed
in the data.
*-e, --err-prob* 'float'::
uniform error probability
*-l, --LRR-weight* 'float'::
relative contribution from LRR. With noisy data, this option can have big effect
on the number of calls produced. In truly random noise (such as in simulated data),
the value should be set high (1.0), but in the presence of systematic noise
when LRR are not informative, lower values result in cleaner calls (0.2).
*-L, --LRR-smooth-win* 'int'::
reduce LRR noise by applying moving average given this window size
*-O, --optimize* 'float'::
iteratively estimate the fraction of aberrant cells, down to the given fraction.
Lowering this value from the default 1.0 to say, 0.3, can help discover more
events but also increases noise
*-P, --same-prob* 'float'::
the prior probability of the query and the control sample being the same.
Setting to 0 calls both independently, setting to 1 forces the same copy
number state in both.
*-x, --xy-prob* 'float'::
the HMM probability of transition to another copy number state. Increasing this
values leads to smaller and more frequent calls.
[[concat]]
=== bcftools concat '[OPTIONS]' 'FILE1' 'FILE2' [...]
Concatenate or combine VCF/BCF files. All source files must have the same sample
columns appearing in the same order. Can be used, for example, to
concatenate chromosome VCFs into one VCF, or combine a SNP VCF and an indel
VCF into one. The input files must be sorted by chr and position. The files
must be given in the correct order to produce sorted VCF on output unless
the *-a, --allow-overlaps* option is specified. With the --naive option, the files
are concatenated without being recompressed, which is very fast..
*-a, --allow-overlaps*::
First coordinate of the next file can precede last record of the current file.
*-c, --compact-PS*::
Do not output PS tag at each site, only at the start of a new phase set block.
*-d, --rm-dups* 'snps'|'indels'|'both'|'all'|'exact'::
Output duplicate records of specified type present in multiple files only once.
Requires *-a, --allow-overlaps*.
*-D, --remove-duplicates*::
Alias for *-d exact*
*-f, --file-list* 'FILE'::
Read file names from 'FILE', one file name per line.
*-l, --ligate*::
Ligate phased VCFs by matching phase at overlapping haplotypes.
Note that the option is intended for VCFs with perfect overlap, sites
in overlapping regions present in one but missing in the other are dropped.
*--ligate-force*::
Keep all sites and ligate even non-overlapping chunks and chunks with imperfect overlap
*--ligate-warn*::
Drop sites in imperfect overlaps
*--no-version*::
see *<<common_options,Common Options>>*
*-n, --naive*::
Concatenate VCF or BCF files without recompression. This is very fast but requires
that all files are of the same type (all VCF or all BCF) and have the same headers.
This is because all tags and chromosome names in the BCF body rely on the order
of the contig and tag definitions in the header. A header check compatibility
is performed and the program throws an error if it is not safe to use the option.
*--naive-force*::
Same as --naive, but header compatibility is not checked. Dangerous, use with caution.
*-o, --output* 'FILE'::
see *<<common_options,Common Options>>*
*-O, --output-type* 'b'|'u'|'z'|'v'::
see *<<common_options,Common Options>>*
*-q, --min-PQ* 'INT'::
Break phase set if phasing quality is lower than 'INT'
*-r, --regions* 'chr'|'chr:pos'|'chr:from-to'|'chr:from-'[,...]::
see *<<common_options,Common Options>>*. Requires *-a, --allow-overlaps*.
*-R, --regions-file* 'FILE'::
see *<<common_options,Common Options>>*. Requires *-a, --allow-overlaps*.
*--threads* 'INT'::
see *<<common_options,Common Options>>*
[[consensus]]
=== bcftools consensus '[OPTIONS]' 'FILE'
Create consensus sequence by applying VCF variants to a reference fasta file.
By default, the program will apply all ALT variants to the reference fasta to
obtain the consensus sequence. Using the *--sample* (and, optionally,
*--haplotype*) option will apply genotype (haplotype) calls from FORMAT/GT.
Note that the program does not act as a primitive variant caller and ignores allelic
depth information, such as INFO/AD or FORMAT/AD. For that, consider using the
*setGT* plugin.
*-c, --chain* 'FILE'::
write a chain file for liftover
*-e, --exclude* 'EXPRESSION'::
exclude sites for which 'EXPRESSION' is true. For valid expressions see
*<<expressions,EXPRESSIONS>>*.
*-f, --fasta-ref* 'FILE'::
reference sequence in fasta format
*-H, --haplotype* '1'|'2'|'R'|'A'|'I'|'LR'|'LA'|'SR'|'SA'|'1pIu'|'2pIu'::
choose which allele from the FORMAT/GT field to use (the codes are case-insensitive):
'1';;
the first allele, regardless of phasing
'2';;
the second allele, regardless of phasing
'R';;
the REF allele (in heterozygous genotypes)
'A';;
the ALT allele (in heterozygous genotypes)
'I';;
IUPAC code for all genotypes
'LR, LA';;
the longer allele. If both have the same length, use the REF allele (LR), or the ALT allele (LA)
'SR, SA';;
the shorter allele. If both have the same length, use the REF allele (SR), or the ALT allele (SA)
'1pIu, 2pIu';;
first/second allele for phased genotypes and IUPAC code for unphased genotypes
This option requires *-s*, unless exactly one sample is present in the VCF
*-i, --include* 'EXPRESSION'::
include only sites for which 'EXPRESSION' is true. For valid expressions see
*<<expressions,EXPRESSIONS>>*.
*-I, --iupac-codes*::
output variants in the form of IUPAC ambiguity codes
*--mark-del* 'CHAR'::
instead of removing sequence, insert CHAR for deletions
*--mark-ins* 'uc'|'lc'::
highlight inserted sequence in uppercase (uc) or lowercase (lc), leaving the rest of the sequence as is
*--mark-snv* 'uc'|'lc'::
highlight substitutions in uppercase (uc) or lowercase (lc), leaving the rest of the sequence as is
*-m, --mask* 'FILE'::
BED file or TAB file with regions to be replaced with N (the default) or as specified by
the next *--mask-with* option. See discussion
of *--regions-file* in *<<common_options,Common Options>>* for file
format details.
*--mask-with* 'CHAR'|'lc'|'uc'::
replace sequence from *--mask* with CHAR, skipping overlapping variants, or change to lowercase (lc) or uppercase (uc)
*-M, --missing* 'CHAR'::
instead of skipping the missing genotypes, output the character CHAR (e.g. "?")
*-o, --output* 'FILE'::
write output to a file
*-s, --sample* 'NAME'::
apply variants of the given sample
*Examples:*
----
# Apply variants present in sample "NA001", output IUPAC codes for hets
bcftools consensus -i -s NA001 -f in.fa in.vcf.gz > out.fa
# Create consensus for one region. The fasta header lines are then expected
# in the form ">chr:from-to".
samtools faidx ref.fa 8:11870-11890 | bcftools consensus in.vcf.gz -o out.fa
----
[[convert]]
=== bcftools convert '[OPTIONS]' 'FILE'
==== VCF input options:
*-e, --exclude* 'EXPRESSION'::
exclude sites for which 'EXPRESSION' is true. For valid expressions see
*<<expressions,EXPRESSIONS>>*.
*-i, --include* 'EXPRESSION'::
include only sites for which 'EXPRESSION' is true. For valid expressions see
*<<expressions,EXPRESSIONS>>*.
*-r, --regions* 'chr'|'chr:pos'|'chr:from-to'|'chr:from-'[,...]::
see *<<common_options,Common Options>>*
*-R, --regions-file* 'FILE'::
see *<<common_options,Common Options>>*
*-s, --samples* 'LIST'::
see *<<common_options,Common Options>>*
*-S, --samples-file* 'FILE'::
see *<<common_options,Common Options>>*
*-t, --targets* 'LIST'::
see *<<common_options,Common Options>>*
*-T, --targets-file* 'FILE'::
see *<<common_options,Common Options>>*
==== VCF output options:
*--no-version*::
see *<<common_options,Common Options>>*
*-o, --output* 'FILE'::
see *<<common_options,Common Options>>*
*-O, --output-type* 'b'|'u'|'z'|'v'::
see *<<common_options,Common Options>>*
*--threads* 'INT'::
see *<<common_options,Common Options>>*
==== GEN/SAMPLE conversion:
*-G, --gensample2vcf* 'prefix' or 'gen-file','sample-file'::
convert IMPUTE2 output to VCF. The second column must be of the form
"CHROM:POS_REF_ALT" to detect possible strand swaps; IMPUTE2 leaves the
first one empty ("--") when sites from reference panel are filled in. See
also *-g* below.
*-g, --gensample* 'prefix' or 'gen-file','sample-file'::
convert from VCF to gen/sample format used by IMPUTE2 and SHAPEIT.
The columns of .gen file format are ID1,ID2,POS,A,B followed by three
genotype probabilities P(AA), P(AB), P(BB) for each sample. In order to
prevent strand swaps, the program uses IDs of the form "CHROM:POS_REF_ALT".
For example:
----
.gen
----
1:111485207_G_A 1:111485207_G_A 111485207 G A 0 1 0 0 1 0
1:111494194_C_T 1:111494194_C_T 111494194 C T 0 1 0 0 0 1
.sample