Provided by: libvcflib-tools_1.0.9+dfsg1-2_amd64 
NAME
vcflib index
DESCRIPTION
vcflib contains tools and libraries for dealing with the Variant Call Format (VCF) which
is a flat-file, tab-delimited textual format intended to describe reference-indexed
variations between individuals.
VCF provides a common interchange format for the description of variation in individuals
and populations of samples, and has become the defacto standard reporting format for a
wide array of genomic variant detectors.
vcflib provides methods to manipulate and interpret sequence variation as it can be
described by VCF. It is both:
• an API for parsing and operating on records of genomic variation as it can be described
by the VCF format,
• and a collection of command-line utilities for executing complex manipulations on VCF
files.
The API itself provides a quick and extremely permissive method to read and write VCF
files. Extensions and applications of the library provided in the included utilities
(*.cpp) comprise the vast bulk of the library’s utility for most users.
filter
filter command description
──────────────────────────────────────────────────────────────────────────
vcffilter VCF filter the specified vcf
file using the set of filters
vcfuniq List unique genotypes.
Similar to GNU uniq, but aimed
at VCF records. vcfuniq
removes records which have the
same position, ref, and alt as
the previous record on a
sorted VCF file. Note that it
does not adjust/combine
genotypes in the output, but
simply takes the first record.
See also vcfcreatemulti for
combining records.
vcfuniqalleles List unique alleles For each
record, remove any duplicate
alternate alleles that may
have resulted from merging
separate VCF files.
metrics
metrics command description
──────────────────────────────────────────────────────────────────────────
vcfcheck Validate integrity and
identity of the VCF by
verifying that the VCF
record’s REF matches a given
reference file.
vcfdistance Adds a tag to each variant
record which indicates the
distance to the nearest
variant. (defaults to
BasesToClosestVariant if no
custom tag name is given.
vcfentropy Annotate VCF records with the
Shannon entropy of flanking
sequence. Anotates the output
VCF file with, for each
record, EntropyLeft,
EntropyRight, EntropyCenter,
which are the entropies of the
sequence of the given window
size to the left, right, and
center of the record. Also
adds EntropyRef and EntropyAlt
for each alt.
vcfhetcount Calculate the heterozygosity
rate: count the number of
alternate alleles in
heterozygous genotypes in all
records in the vcf file
vcfhethomratio Generates the het/hom ratio
for each individual in the
file
phenotype
phenotype command description
──────────────────────────────────────────────────────────────────────────
permuteGPAT++ permuteGPAT++ is a method for
adding empirical p-values to a
GPAT++ score.
genotype
genotype command description
──────────────────────────────────────────────────────────────────────────
abba-baba abba-baba calculates the tree
pattern for four indviduals.
This tool assumes reference is
ancestral and ignores non
abba-baba sites. The output
is a boolian value: 1 = true ,
0 = false for abba and baba.
the tree argument should be
specified from the most basal
taxa to the most derived.
hapLrt HapLRT is a likelihood ratio
test for haplotype lengths.
The lengths are modeled with
an exponential distribution.
The sign denotes if the target
has longer haplotypes (1) or
the background (-1).
normalize-iHS normalizes iHS or XP-EHH
scores.
transformation
transformation command description
──────────────────────────────────────────────────────────────────────────
dumpContigsFromHeader Dump contigs from header
smoother smoothes is a method for
window smoothing many of the
GPAT++ formats.
vcf2dag Modify VCF to be able to build
a directed acyclic graph (DAG)
vcf2fasta Generates sample_seq:N.fa for
each sample, reference
sequence, and chromosomal copy
N in [0,1... ploidy]. Each
sequence in the fasta file is
named using the same pattern
used for the file name,
allowing them to be combined.
vcf2tsv Converts VCF to per-allelle or
per-genotype tab-delimited
format, using null string to
replace empty values in the
table. Specifying -g will
output one line per sample
with genotype information.
When there is more than one
alt allele there will be
multiple rows, one for each
allele and, the info will
match the `A' index
vcfaddinfo Adds info fields from the
second file which are not
present in the first vcf file.
vcfafpath Display genotype paths
vcfallelicprimitives WARNING: this tool is
considered legacy and is only
retained for older workflows.
It will emit a warning! Even
though it can use the WFA you
should use vcfwave instead.
vcfannotate Intersect the records in the
VCF file with targets provided
in a BED file. Intersections
are done on the reference
sequences in the VCF file. If
no VCF filename is specified
on the command line (last
argument) the VCF read from
stdin.
vcfannotategenotypes Examine genotype
correspondence. Annotate
genotypes in the first file
with genotypes in the second
adding the genotype as another
flag to each sample filed in
the first file. annotation-
tag is the name of the sample
flag which is added to store
the annotation. also adds a
`has_variant' flag for sites
where the second file has a
variant.
vcfbreakmulti If multiple alleles are
specified in a single record,
break the record into multiple
lines, preserving allele-
specific INFO fields.
vcfcat Concatenates VCF files
vcfclassify Creates a new VCF where each
variant is tagged by allele
class: snp, ts/tv, indel, mnp
vcfcleancomplex Removes reference-matching
sequence from complex alleles
and adjusts records to reflect
positional change.
vcfcombine Combine VCF files
positionally, combining
samples when sites and alleles
are identical. Any number of
VCF files may be combined.
The INFO field and other
columns are taken from one of
the files which are combined
when records in multiple files
match. Alleles must have
identical ordering to be
combined into one record. If
they do not, multiple records
will be emitted.
vcfcommonsamples Generates each record in the
first file, removing samples
not present in the second
vcfcreatemulti Go through sorted VCF and when
overlapping alleles are
represented across multiple
records, merge them into a
single multi-ALT record. See
the documentation for more
information.
vcfecho Echo VCF to stdout (simple
demo)
vcfevenregions Generates a list of regions,
e.g. chr20:10..30 using the
variant density information
provided in the VCF file to
ensure that the regions have
even numbers of variants.
This can be use to reduce the
variance in runtime when
dividing variant detection or
genotyping by genomic
coordinates.
vcffixup Generates a VCF stream where
AC and NS have been generated
for each record using sample
genotypes
vcfflatten Removes multi-allelic sites by
picking the most common
alternate. Requires allele
frequency specification `AF'
and use of `G' and `A' to
specify the fields which vary
according to the Allele or
Genotype. VCF file may be
specified on the command line
or piped as stdin.
vcfgeno2alleles modifies the genotypes field
to provide the literal alleles
rather than indexes
vcfgeno2haplo Convert genotype-based phased
alleles within –window-size
into haplotype alleles. Will
break haplotype construction
when encountering non-phased
genotypes on input.
vcfgenosamplenames Get samplenames
vcfglbound Adjust GLs so that the maximum
GL is 0 by dividing all GLs
for each sample by the max.
vcfglxgt Set genotypes using the
maximum genotype likelihood
for each sample.
vcfindex Adds an index number to the
INFO field (id=position)
vcfinfo2qual Sets QUAL from info field tag
keyed by [key]. The VCF file
may be omitted and read from
stdin. The average of the
field is used if it contains
multiple values.
vcfinfosummarize Take annotations given in the
per-sample fields and add the
mean, median, min, or max to
the site-level INFO.
vcfintersect VCF set analysis
vcfkeepgeno Reduce file size by removing
FORMAT fields not listed on
the command line from sample
specifications in the output
vcfkeepinfo To decrease file size remove
INFO fields not listed on the
command line
vcfkeepsamples outputs each record in the vcf
file, removing samples not
listed on the command line
vcfld Compute LD
vcfleftalign Left-align indels and complex
variants in the input using a
pairwise ref/alt alignment
followed by a heuristic,
iterative left realignment
process that shifts indel
representations to their
absolute leftmost (5’) extent.
vcflength Add length info field
vcfnullgenofields Makes the FORMAT for each
variant line the same (uses
all the FORMAT fields
described in the header).
Fills out per-sample fields to
match FORMAT. Expands GT
values of `.' with number of
alleles based on ploidy (eg:
`./.' for dipolid).
vcfnumalt outputs a VCF stream where
NUMALT has been generated for
each record using sample
genotypes
vcfoverlay Overlay records in the input
vcf files with order as
precedence.
vcfprimers For each VCF record, extract
the flanking sequences, and
write them to stdout as FASTA
records suitable for
alignment.
vcfqual2info Puts QUAL into an info field
tag keyed by [key].
vcfremap For each alternate allele,
attempt to realign against the
reference with lowered gap
open penalty. If realignment
is possible, adjust the cigar
and reference/alternate
alleles. Observe how
different alignment
parameters, including context
and entropy-dependent ones,
influence variant
classification and
interpretation.
vcfremoveaberrantgenotypes strips samples which are
homozygous but have
observations implying
heterozygosity. Remove
samples for which the reported
genotype (GT) and observation
counts disagree (AO, RO).
vcfremovesamples outputs each record in the vcf
file, removing samples listed
on the command line
vcfsample2info Take annotations given in the
per-sample fields and add the
mean, median, min, or max to
the site-level INFO.
vcfsamplediff Establish putative somatic
variants using reported
differences between germline
and somatic samples. Tags
each record where the listed
sample genotypes differ with .
The first sample is assumed to
be germline, the second
somatic. Each record is
tagged with
={germline,somatic,loh} to
specify the type of variant
given the genotype difference
between the two samples.
vcfsamplenames List sample names
vcfstreamsort Sorts the input (either stdin
or file) using a streaming
sort algorithm. Guarantees
that the positional order is
correct provided out-of-order
variants are no more than 100
positions in the VCF file
apart.
vcfwave Realign reference and
alternate alleles with WFA,
parsing out the `primitive'
alleles into multiple VCF
records. New records have IDs
that reference the source
record ID. Genotypes/samples
are handled correctly.
Deletions generate
haploid/missing genotypes at
overlapping sites.
statistics
statistics command description
──────────────────────────────────────────────────────────────────────────
bFst bFst is a Bayesian approach to
Fst. Importantly bFst
accounts for genotype
uncertainty in the model using
genotype likelihoods. For a
more detailed description see:
`A Bayesian approach to
inferring population structure
from dominant markers’ by
Holsinger et al. Molecular
Ecology Vol 11, issue 7 2002.
The likelihood function has
been modified to use genotype
likelihoods provided by
variant callers. There are
five free parameters estimated
in the model: each
subpopulation’s allele
frequency and Fis (fixation
index, within each
subpopulation), a free
parameter for the total
population’s allele frequency,
and Fst.
genotypeSummary Generates a table of genotype
counts. Summarizes genotype
counts for bi-allelic SNVs and
indel
iHS iHS calculates the integrated
haplotype score which measures
the relative decay of extended
haplotype homozygosity (EHH)
for the reference and
alternative alleles at a site
(see: voight et al. 2006,
Spiech & Hernandez 2014).
meltEHH
pFst pFst is a probabilistic
approach for detecting
differences in allele
frequencies between two
populations.
pVst pVst calculates vst, a measure
of CNV stratification.
permuteSmooth permuteSmooth is a method for
adding empirical p-values
smoothed wcFst scores.
plotHaps plotHaps provides the
formatted output that can be
used with
`bin/plotHaplotypes.R'.
popStats General population genetic
statistics for each SNP
segmentFst segmentFst creates genomic
segments (bed file) for
regions with high wcFst
segmentIhs Creates genomic segments (bed
file) for regions with high
wcFst
sequenceDiversity The sequenceDiversity program
calculates two popular metrics
of haplotype diversity: pi and
extended haplotype
homozygoisty (eHH). Pi is
calculated using the Nei and
Li 1979 formulation. eHH a
convenient way to think about
haplotype diversity. When eHH
= 0 all haplotypes in the
window are unique and when eHH
= 1 all haplotypes in the
window are identical.
vcfaltcount count the number of alternate
alleles in all records in the
vcf file
vcfcountalleles Count alleles
vcfgenosummarize Adds summary statistics to
each record summarizing
qualities reported in called
genotypes. Uses: RO
(reference observation count),
QR (quality sum reference
observations) AO (alternate
observation count), QA
(quality sum alternate
observations)
vcfgenotypecompare adds statistics to the INFO
field of the vcf file
describing the amount of
discrepancy between the
genotypes (GT) in the vcf file
and the genotypes reported in
the . use this after
vcfannotategenotypes to get
correspondence statistics for
two vcfs.
vcfgenotypes Report the genotypes for each
sample, for each variant in
the VCF. Convert the
numerical represenation of
genotypes provided by the GT
field to a human-readable
genotype format.
vcfparsealts Alternate allele parsing
method. This method uses
pairwise alignment of REF and
ALTs to determine component
allelic primitives for each
alternate allele.
vcfrandom Generate a random VCF file
vcfrandomsample Randomly sample sites from an
input VCF file, which may be
provided as stdin. Scale the
sampling probability by the
field specified in KEY. This
may be used to provide uniform
sampling across allele
frequencies, for instance.
vcfroc Generates a pseudo-ROC curve
using sensitivity and
specificity estimated against
a putative truth set.
Thresholding is provided by
successive QUAL cutoffs.
vcfsitesummarize Summarize by site
vcfstats Prints statistics about
variants in the input VCF
file.
wcFst wcFst is Weir & Cockerham’s
Fst for two populations.
Negative values are VALID,
they are sites which can be
treated as zero Fst. For more
information see Evolution,
Vol. 38 N. 6 Nov 1984.
Specifically wcFst uses
equations 1,2,3,4.
SOURCE CODE
See the source code repository at https://github.com/vcflib/vcflib
CREDIT
Citations are the bread and butter of Science. If you are using this software in your
research and want to support our future work, please cite the following publication:
Please cite:
A spectrum of free software tools for processing the VCF variant call format: vcflib, bio-
vcf, cyvcf2, hts-nim and slivar
(https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1009123).
Garrison E, Kronenberg ZN, Dawson ET, Pedersen BS, Prins P (2022), PLoS Comput Biol 18(5):
e1009123. https://doi.org/10.1371/journal.pcbi.1009123
LICENSE
Copyright 2011-2023 (C) Erik Garrison and vcflib contributors. MIT licensed.
AUTHORS
Erik Garrison and vcflib contributors.