bcftools(1) Manual Page

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.

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  -c indels), or only sites with all alleles identical (bcftools isec -c none).

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.

Do not append version and command line information to the output VCF header.

When output consists of a single stream, write it to FILE rather than to standard output, where it is written by default. The file type is determined automatically from the file name suffix and in case a conflicting -O option is given, the file name suffix takes precedence.

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.   The compression level of the compressed formats (b and z) can be set by by appending a number between 0-9.

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.

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: CHROM, POS) or intervals (three-column format: CHROM, BEG, END), but not both. 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.

This option controls how overlapping records are determined: set to pos or 0 if the VCF record has to have POS inside a region (this corresponds to the default behavior of -t/-T); set to record or 1 if also overlapping records with POS outside a region should be included (this is the default behavior of -r/-R, and includes indels with POS at the end of a region, which are technically outside the region); or set to variant or 2 to include only true overlapping variation (compare the full VCF representation "TA>T-" vs the true sequence variation "A>-").

Comma-separated list of samples to include or exclude if prefixed with "^." (Note that when multiple samples are to be excluded, the "^" prefix is still present only once, e.g. "^SAMPLE1,SAMPLE2".) 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. bcftools view is the exception where some tags will be updated (unless the -I, --no-update option is used; see bcftools view documentation). To use updated tags for the subset in another command one can pipe from view into that command. For example:

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 bcftools call accepts an optional second column indicating ploidy (0, 1 or 2) or sex (as defined by --ploidy, for example "F" or "M"), for example:

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 (by default; see also --regions-overlap and --targets-overlap). Note that -t cannot be used in combination with -T.

Same -t, --targets, but reads regions from a file. Note that -T cannot be used in combination with -t.

Same as --regions-overlap but for -t/-T.

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.

Automatically index the output files. FMT is optional and can be one of "tbi" or "csi" depending on output file format. Defaults to CSI unless specified otherwise. Can be used only for compressed BCF and VCF output.

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.  
 
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.  
 
Missing values can be added by providing "." in place of actual value and using the missing value modifier with -c, such as ".TAG".  
 
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.

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,TO or BEG,END), and optionally REF and ALT. Unused columns which should be ignored can be indicated by "-".  
 
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".  
 
To carry over all INFO annotations, use "INFO". To add all INFO annotations except "TAG", use "^INFO/TAG". By default, existing values are replaced.  
 
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". As a special case of this, if position needs to be replaced, mark the column with the new coordinate as "-POS". (Note that in previous releases this used to be "~POS", now deprecated.)  
 
To match the record also by ID or INFO/END, in addition to REF and ALT, use "~ID" or "~INFO/END". Note that this works only for ID and POS, for other fields see the description of -i below.  
 
If the annotation file is not a VCF/BCF, all new annotations must be defined via -h, --header-lines.  
 
See also the -l, --merge-logic option.  
 
Summary of -c, --columns:

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.

exclude sites for which EXPRESSION is true. For valid expressions see EXPRESSIONS and the extension described in -i, --include below.

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.

Lines to append to the VCF header, see also -c, --columns and -a, --annotations. For example:

assign ID on the fly. The format is the same as in the 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

include only sites for which EXPRESSION is true. For valid expressions see EXPRESSIONS.  
 
Additionally, the command bcftools annotate supports expressions updated from the annotation file dynamically for each record:

keep sites which do not pass -i and -e expressions instead of discarding them

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.

annotate sites which are present ("+") or absent ("-") in the -a file with a new INFO/TAG flag

minimum overlap required as a fraction of the variant in the annotation -a file (ANN), in the target VCF file (:VCF), or both for reciprocal overlap (ANN:VCF). By default overlaps of arbitrary length are sufficient. The option can be used only with the tab-delimited annotation -a file and with BEG and END columns present.

see Common Options

see Common Options

see Common Options

Controls how to match records from the annotation file to the target VCF. Effective only when -a is a VCF or BCF. The option replaces the former uninuitive --collapse. See Common Options for more.

see Common Options

see Common Options

see Common Options

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 chromosomes according to the map in file, with "old_name new_name\n" pairs separated by whitespaces, each on a separate line.

subset of samples to annotate, see also Common Options

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.

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).

see Common Options

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".

Automatically index the output file. FMT is optional and can be one of "tbi" or "csi" depending on output file format.

First coordinate of the next file can precede last record of the current file.

Do not output PS tag at each site, only at the start of a new phase set block.

Output duplicate records of specified type present in multiple files only once. Note that records duplicate within one file are not removed with this option, for that use bcftools norm -d instead.
In other words, the default behavior of the program is similar to unix "cat" in that when two files contain a record with the same position, that position will appear twice on output. With -d, every line that finds a matching record in another file will be printed only once.
Requires -a, --allow-overlaps.

Alias for -d exact

Read file names from FILE, one file name per line.

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.

Keep all sites and ligate even non-overlapping chunks and chunks with imperfect overlap

Drop sites in imperfect overlaps

see Common Options

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.

Same as --naive, but header compatibility is not checked. Dangerous, use with caution.

see Common Options

see Common Options

Break phase set if phasing quality is lower than INT

see Common Options. Requires -a, --allow-overlaps.

see Common Options. Requires -a, --allow-overlaps.

see Common Options

see Common Options

Automatically index the output file. FMT is optional and can be one of "tbi" or "csi" depending on output file format.

replace positions absent from VCF with CHAR

write a chain file for liftover

exclude sites for which EXPRESSION is true. For valid expressions see EXPRESSIONS.

reference sequence in fasta format

choose which allele from the FORMAT/GT field to use (the codes are case-insensitive):

include only sites for which EXPRESSION is true. For valid expressions see EXPRESSIONS.

output variants in the form of IUPAC ambiguity codes determined from FORMAT/GT fields. By default all samples are used and can be subset with -s, --samples and -S, --samples-file. Use -s - to ignore samples and use only the REF and ALT columns. NOTE: prior to version 1.17 the IUPAC codes were determined solely from REF,ALT columns and sample genotypes were not considered.

instead of removing sequence, insert character CHAR for deletions

highlight inserted sequence in uppercase (uc), lowercase (lc), or a provided character CHAR, leaving the rest of the sequence as is

highlight substitutions in uppercase (uc), lowercase (lc), or a provided character CHAR, leaving the rest of the sequence as is

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 for file format details.

replace sequence from --mask with CHAR, skipping overlapping variants, or change to lowercase (lc) or uppercase (uc)

instead of skipping the missing genotypes, output the character CHAR (e.g. "?")

write output to a file

how to treat VCF variants overlapping the target region in the fasta file: see Common Options

apply variants of the listed samples. See also the option -I, --iupac-codes

apply variants of the samples listed in the file. See also the option -I, --iupac-codes

Masking options are applied in the following order

use this custom tag to store consequences rather than the default BCSQ tag

abbreviate protein-changing predictions to maximum of INT aminoacids. For example, instead of writing the whole modified protein sequence with potentially hundreds of aminoacids, with -B 1 only an abbreviated version such as 25E..329>25G..94 will be written.

dump the parsed GFF into a gzipped FILE. Intended for debugging purposes, shows how is the input GFF viewed by the program.

exclude sites for which EXPRESSION is true. For valid expressions see EXPRESSIONS.

reference sequence in fasta format (required)

run even if some sanity checks fail. Currently the option enables skipping transcripts in malformatted GFFs with incorrect phase

GFF3 annotation file (required), such as http://ftp.ensembl.org/pub/current_gff3/homo_sapiens/. The script gff2gff can help with conversion from non-standard GFF formats. An example of a minimal working GFF file:

include only sites for which EXPRESSION is true. For valid expressions see EXPRESSIONS.

switch off haplotype-aware calling, run localized predictions considering only one VCF record at a time

maximum number of per-haplotype consequences to consider for each site. The INFO/BCSQ column includes all consequences, but only the first INT will be referenced by the FORMAT/BCSQ fields. The default value is 15 which corresponds to one 32-bit integer per diploid sample, after accounting for values reserved by the BCF specification. Note that increasing the value leads to increased size of the output BCF.

see Common Options

see Common Options

see Common Options. In addition, a custom tab-delimited plain text output can be printed (t).

how to handle unphased heterozygous genotypes:

suppress warning messages

see Common Options

see Common Options

see Common Options

samples to include or "-" to apply all variants and ignore samples

see Common Options

see Common Options

see Common Options

see Common Options

Automatically detect and unify chromosome naming conventions in the GFF, fasta and VCF, such as "chrX" vs "X". The chromosome names in the output VCF will match that of the input VCF. The default is to attempt the automatic translation.

verbosity level (0-2)

Automatically index the output file. FMT is optional and can be one of "tbi" or "csi" depending on output file format.

exclude sites for which EXPRESSION is true. For valid expressions see EXPRESSIONS.

filter SNPs within INT base pairs of an indel or other other variant type. The following example demonstrates the logic of --SnpGap 3 applied on a deletion and an insertion:

filter clusters of indels separated by INT or fewer base pairs allowing only one to pass. The following example demonstrates the logic of --IndelGap 2 applied on a deletion and an insertion:

include only sites for which EXPRESSION is true. For valid expressions see EXPRESSIONS.

Soft filter regions, prepepend "^" to negate. Requires -s, --soft-filter.

Soft filter regions listed in a file, "^" to negate. Requires -s, --soft-filter.

Same as --regions-overlap but for --mask/--mask-file. See Common Options. [1]

define behaviour at sites with existing FILTER annotations. The default mode replaces existing filters of failed sites with a new FILTER string while leaving sites which pass untouched when non-empty and setting to "PASS" when the FILTER string is absent. The "+" mode appends new FILTER strings of failed sites instead of replacing them. The "x" mode resets filters of sites which pass to "PASS". Modes "+" and "x" can both be set.

see Common Options

see Common Options

see Common Options

see Common Options

see Common Options

see Common Options

annotate FILTER column with STRING or, with +, a unique filter name generated by the program ("Filter%d"). Applies to records that do not meet filter expression.

set genotypes of failed samples to missing value (.) or reference allele (0)

see Common Options

see Common Options

see Common Options

see Common Options

Automatically index the output file. FMT is optional and can be one of "tbi" or "csi" depending on output file format.

Find sites that can distinguish between at least NUM sample pairs. If the number is smaller or equal to 1, it is interpreted as the fraction of pairs. The optional MEM string sets the maximum memory used for in-memory sorting and DIR is the temporary directory for external sorting. This option requires also --pairs to be given.

Stop after first record to estimate required time.

Exclude sites from query file (qry:) or genotype file (gt:) for which EXPRESSION is true. For valid expressions see EXPRESSIONS.

Interpret genotypes and genotype likelihoods probabilistically. The value of INT represents genotype quality when GT tag is used (e.g. Q=30 represents one error in 1,000 genotypes and Q=40 one error in 10,000 genotypes) and is ignored when PL tag is used (in that case an arbitrary non-zero integer can be provided).  
 
If -E is set to 0, the discordance score can be interpreted as the number of mismatching genotypes, but only in the GT-vs-GT matching mode. See the -u, --use option below for additional notes and caveats.  
 
If performance is an issue, set -E 0 for faster run times but less accurate results.  
 
Note that in previous versions of bcftools (⇐1.18), this option used to be a smaller case -e. It changed to make room for the filtering option -e, --exclude to stay consistent across other commands.

VCF/BCF file with reference genotypes to compare against

Homozygous genotypes only, useful with low coverage data (requires -g, --genotypes)

Include sites from query file (qry:) or genotype file (gt:) for which EXPRESSION is true. For valid expressions see EXPRESSIONS.

Print only top INT matches for each sample, 0 for unlimited. Use negative value to sort by HWE probability rather than the number of discordant sites. Note that average score is used to determine the top matches, not absolute values.

Disable calculation of HWE probability to reduce memory requirements with comparisons between very large number of sample pairs.

Write to FILE rather than to standard output, where it is written by default.

Write a plain (t) or compressed (z) text tab-delimited output.

A comma-separated list of sample pairs to compare. When the -g option is given, the first sample must be from the query file, the second from the -g file, third from the query file etc (qry,gt[,qry,gt..]). Without the -g option, the pairs are created the same way but both samples are from the query file (qry,qry[,qry,qry..])

A file with tab-delimited sample pairs to compare. The first sample in the pair must come from the query file, the second from the genotypes file when -g is given

Restrict to comma-separated list of regions, see Common Options

Restrict to regions listed in a file, see Common Options

see Common Options

see Common Options

see Common Options

see Common Options

specifies which tag to use in the query file (TAG1) and the -g (TAG2) file. By default, the PL tag is used in the query file and, when available, the GT tags in the -g file.  
 
Note that when the requested tag is not available, the program will attempt to use the other tag. The output includes the number of sites that were matched by the four possible modes (for example GT-vs-GT or GT-vs-PL).

see Common Options

output positions present only in the first file but missing in the others

exclude sites for which EXPRESSION is true. If -e (or -i) appears only once, the same filtering expression will be applied to all input files. Otherwise, -e or -i must be given for each input file. To indicate that no filtering should be performed on a file, use "-" in place of EXPRESSION, as shown in the example below. For valid expressions see EXPRESSIONS.

see Common Options

include only sites for which EXPRESSION is true. See discussion of -e, --exclude above.

Read file names from FILE, one file name per line.

output positions present in this many (=), this many or more (+), this many or fewer (-), or the exact same (~) files

see Common Options. When several files are being output, their names are controlled via -p instead.

see Common Options

if given, subset each of the input files accordingly. See also -w.

see Common Options

see Common Options

see Common Options

see Common Options

see Common Options

see Common Options

comma-separated list of input files to output given as 1-based indices. With -p and no -w, all files are written.

Automatically index the output file. FMT is optional and defaults to tbi for vcf.gz and csi for bcf. This is done automatically with the -p option if the output format is compressed.

synonymous to --no-index

if the merged files contain duplicate samples names, proceed anyway. Duplicate sample names will be resolved by prepending the index of the file as it appeared on the command line to the conflicting sample name (see 2:S3 in the above example).

run even if only one file is given on input

print only merged header and exit

use the VCF header in the provided text FILE

assume genotypes at missing sites are 0/0

see Common Options

Set the output record to PASS if any of the inputs is PASS (x), or apply all filters (+), which is the default.

merge gVCF blocks, INFO/END tag is expected. If the reference fasta file FILE is not given and the dash (-) is given, unknown reference bases generated at gVCF block splits will be substituted with N’s. The --gvcf option uses the following default INFO rules: -i QS:sum,MinDP:min,I16:sum,IDV:max,IMF:max and the following missing rules: -M PL:max,AD:0.

Rules for merging INFO fields (scalars or vectors) or - to disable the default rules. METHOD is one of sum, avg, min, max, join. Default is DP:sum,DP4:sum if these fields exist in the input files. Fields with no specified rule will take the value from the first input file. The merged QUAL value is currently set to the maximum. This behaviour is not user controllable at the moment.

Read file names from FILE, one file name per line.

Sites with many alternate alleles can require extremely large storage space which can exceed the 2GB size limit representable by BCF. This is caused by Number=G tags (such as FORMAT/PL) which store a value for each combination of reference and alternate alleles. The -L, --local-alleles option allows replacement of such tags with a localized tag (FORMAT/LPL) which only includes a subset of alternate alleles relevant for that sample. A new FORMAT/LAA tag is added which lists 1-based indices of the alternate alleles relevant (local) for the current sample. The number INT gives the maximum number of alternate alleles that can be included in the PL tag. The default value is 0 which disables the feature and outputs values for all alternate alleles.

The option controls what types of multiallelic records can be created. If single asterisk * is appended, the unobserved allele <*> or <NON_REF> will be removed at variant sites; if two asterisks ** are appended, the unobserved allele will be removed all sites.

Rules for merging vector tags at multiallelic sites. When input files have different alternate alleles, vector fields pertaining to unobserved alleles are set to missing (.) by default. The METHOD is one of . (the default, use missing values), NUMBER (use a constant value, e.g. 0), max (the maximum value observed for other alleles in the sample). When --gvcf option is set, the rule -M PL:max,AD:0 is implied. This can be overridden with providing -M - or -M PL:.,AD:.. Note that if the unobserved allele is explicitly present as <*> or <NON_REF>, then its corresponding value will be used regardless of -M settings.

the option allows files to be merged without indexing them first. In order for this option to work, the user must ensure that the input files have chromosomes in the same order and consistent with the order of sequences in the VCF header.

see Common Options

see Common Options

see Common Options

see Common Options

see Common Options

see Common Options

see Common Options

Automatically index the output file. FMT is optional and can be one of "tbi" or "csi" depending on output file format.

Decompose complex variants, e.g. split MNVs into consecutive SNVs. See also --atom-overlaps and --old-rec-tag.

Alleles missing because of an overlapping variant can be set either to missing (.) or to the star alele (*), as recommended by the VCF specification. IMPORTANT: Note that asterisk is expaneded by shell and must be put in quotes or escaped by a backslash:

what to do when incorrect or missing REF allele is encountered: exit (e), warn (w), exclude (x), or set/fix (s) bad sites. The w option can be combined with x and s. Note that s can swap alleles and will update genotypes (GT) and AC counts, but will not attempt to fix PL or other fields. Also note, and this cannot be stressed enough, that s will NOT fix strand issues in your VCF, do NOT use it for that purpose!!! (Instead see http://samtools.github.io/bcftools/howtos/plugin.af-dist.html and <http://samtools.github.io/bcftools/howtos/plugin.fixref.html>.)

If a record is present multiple times, output only the first instance. See also --collapse in Common Options.

If a record is present in multiple files, output only the first instance. Alias for -d exact, deprecated.

do not normalize input records for which EXPRESSION is true. For valid expressions see EXPRESSIONS. Note that duplicate removal ignores this option.

reference sequence. Supplying this option will turn on left-alignment and normalization, however, see also the --do-not-normalize option below.

try to proceed with -m- even if malformed tags with incorrect number of fields are encountered, discarding such tags. (Experimental, use at your own risk.)

when a GFF file is provided, follow HGVS 3’rule and right-align variants in transcripts on the forward strand. In case of overlapping transcripts, the default mode is to left-align the variant. For a description of the supported GFF3 file format see bcftools csq.

normalize only input records for which EXPRESSION is true. For valid expressions see EXPRESSIONS. Note that duplicate removal ignores this option.

keep vector sum constant when splitting multiallelic sites. Only AD tag is currently supported. See also https://github.com/samtools/bcftools/issues/360

split multiallelic sites into biallelic records (-) or join biallelic sites into multiallelic records (+). An optional type string can follow which controls variant types which should be split or merged together: If only SNP records should be split or merged, specify snps; if both SNPs and indels should be merged separately into two records, specify both; if SNPs and indels should be merged into a single record, specify any.  
 
Note that multiallelic sites with both SNPs and indels will be split into biallelic sites with both -m -snps and -m -indels.

use the reference (0) or missing (.) allele for overlapping alleles after splitting multiallelic sites

see Common Options

the -c s option can be used to fix or set the REF allele from the reference -f. The -N option will not turn on indel normalisation as the -f option normally implies

Add INFO/STR annotation with the original record. The format of the annotation is CHROM|POS|REF|ALT|USED_ALT_IDX.

see Common Options

see Common Options

see Common Options

see Common Options

see Common Options

when merging (-m+), merged site is PASS only if all sites being merged PASS

when splitting sites or processing duplicates, sort records on output by POS only (pos, the default) or by POS and lexicographically by REF+ALT (lex)

see Common Options

see Common Options

see Common Options

see Common Options

verbosity level of GFF parsing (0-2)

maximum distance between two records to consider when locally sorting variants which changed position during the realignment

Automatically index the output file. FMT is optional and can be one of "tbi" or "csi" depending on output file format.

exclude sites for which EXPRESSION is true. For valid expressions see EXPRESSIONS.

continue even when some samples requested via -s/-S do not exist

learn by example, see below

by default, samples failing -i/-e filtering expressions are suppressed from output when FORMAT fields are queried (for example %CHROM %POS [ %GT]). With -F, such fields will be still printed but instead of their actual value, STR will be used.

print header. By default, the header is printed with column indices, e.g. "#[1]CHROM". These can be suppressed by giving the option twice, "-HH".

include only sites for which EXPRESSION is true. For valid expressions see EXPRESSIONS.

list sample names and exit

disable automatic addition of a missing newline character at the end of the formatting expression. By default, the program checks if the expression contains a newline and appends it if not, to prevent formatting the entire output into a single line by mistake. Note that versions prior to 1.18 had no automatic check and newline had to be included explicitly.

see Common Options

see Common Options

see Common Options

see Common Options

see Common Options

see Common Options

see Common Options

see Common Options

see Common Options

do not throw an error if there are undefined tags in the format string, print "." instead

process multiple VCFs listed in the file

add to the header contig names and their lengths from the provided fasta index file (.fai). Lengths of existing contig lines will be updated and contig lines not present in the fai file will be removed

new VCF header

see Common Options

new sample names, one name per line, in the same order as they appear in the VCF file. Alternatively, only samples which need to be renamed can be listed as "old_name new_name\n" pairs separated by whitespaces, each on a separate line. If a sample name contains spaces, the spaces can be escaped using the backslash character, for example "Not\ a\ good\ sample\ name".

this option is ignored, but left for compatibility with earlier versions of bcftools.

see Common Options

Maximum memory to use. Approximate, affects the number of temporary files written to the disk. Note that if the command fails at this step because of too many open files, your system limit on the number of open files ("ulimit") may need to be increased.

see Common Options

see Common Options

Use this directory to store temporary files. If the last six characters of the string DIR are XXXXXX, then these are replaced with a string that makes the directory name unique.

Automatically index the output file. FMT is optional and can be one of "tbi" or "csi" depending on output file format.

comma separated list of allele frequency bins (e.g. 0.1,0.5,1) or a file listing the allele frequency bins one per line (e.g. 0.1\n0.5\n1)

allele frequency INFO tag to use for binning. By default the allele frequency is estimated from AC/AN, if available, or directly from the genotypes (GT) if not.

consider only the 1st alternate allele at multiallelic sites

see Common Options

ranges of depth distribution: min, max, and size of the bin

produce verbose per-site and per-sample output

exclude sites for which EXPRESSION is true. For valid expressions see EXPRESSIONS.

tab-delimited file with exons for indel frameshifts statistics. The columns of the file are CHR, FROM, TO, with 1-based, inclusive, positions. The file is BGZF-compressed and indexed with tabix

see Common Options

faidx indexed reference sequence file to determine INDEL context

include only sites for which EXPRESSION is true. For valid expressions see EXPRESSIONS.

collect stats separately for sites which have the ID column set ("known sites") or which do not have the ID column set ("novel sites").

see Common Options

see Common Options

see Common Options

see Common Options

see Common Options

see Common Options

see Common Options

see Common Options

collect Ts/Tv stats for any tag using the given binning [0:1:100]

produce verbose per-site and per-sample output

Merge vcfstats files to STDOUT, skip plotting.

The output directory. This directory will be created if it does not exist.

Skip the PDF creation step.

Rasterize PDF images for faster rendering. This is the default and the opposite of -v, --vectors.

Use sample names for xticks rather than numeric IDs.

Identify files by these titles in plots. The option can be given multiple times, for each ID in the bcftools stats output. If not present, the script will use abbreviated source file names for the titles.

Generate vector graphics for PDF images, the opposite of -r, --rasterize.

Main title for the PDF.