Provided by: libbio-db-hts-perl_3.01-3build2_amd64 
LICENSE
Copyright [2015-2018] EMBL-European Bioinformatics Institute
Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file
except in compliance with the License. You may obtain a copy of the License at
http://www.apache.org/licenses/LICENSE-2.0
Unless required by applicable law or agreed to in writing, software distributed under the
License is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND,
either express or implied. See the License for the specific language governing
permissions and limitations under the License.
AUTHORS
Rishi Nag <rishi@ebi.ac.uk>, original author.
Alessandro Vullo "<avullo at cpan.org>", the current developer and maintainer.
NAME
Bio::DB::HTS::VCF -- Read VCF/BCF data files
DESCRIPTION
This module provides a Perl interface to the HTSlib library for reading variant calls
stored in VCF and BCF file databases.
The functions provided are for opening a VCF/BCF file, reading header values, querying
specific chromosome intervals and then reading row values.
A sweep set of methods allows running through rows one by one, either backwards or
forwards through the file.
SYNOPSIS
use Bio::DB::HTS::VCF ;
### File Open ###
my $v = Bio::DB::HTS::VCF->new( filename => "/path/to/myfile.vcf.gz" );
# once the file has been opened, various global values can be read from the header
my $h = $v->header();
$h->get_seqnames() ;
$h->version() ; # read the VCF file version
$h->num_samples() ;
$h->get_sample_names() ; #return an array of sample names
$h->num_seqnames() ;
$h->get_seqnames() ; # return an array of sequence names
### Individual rows can be read in and fields accessed ###
my $row = $v->next() ;
# row functions
$row->chromosome($h) ;
$row->position() ;
$row->id() ;
$row->num_filters() ;
$row->quality() ;
# retrieve alleles
my $num_alleles = $row->num_alleles();
my $alleles = $row->get_alleles();
my $allele_index = 1;
for my $a (@$alleles) {
printf( "(%s, %s)\n", $a, $row->get_variant_type($allele_index++) ) ;
}
# query filters
$row->has_filter($h,"DP50");
$row->has_filter($h,"."); # PASS filter check
$row->get_info_type($h, "AF"); # one of "String", "Integer", "Float" or "Flag".
$info_result = $row->get_info($h, "NS"); # [3]
$row->get_format_type($h, "GT") ; # "String"
$row->get_format($h, "DP") ; # [ 1, 8, 5 ]
### free memory associated with the row
Bio::DB::HTS::VCF::Row->destroy($row);
### query specific locations
my $iter = $v->query("20:1000000-1231000");
while (my $result = $iter->next) {
print $result->chromosome($h), $result->position(), $result->id(), $result->num_filters(), $result->quality(), "\n";
}
METHODS
"new"
Opens a VCF/BCF file for reading. If the file is indexed (i.e. tabix for VCF, csi for BCF)
the index is opened and used for querying arbitrary locations on the chromosomes.
$vcf = Bio::DB::HTS::VCF->new($filepath)
Returns an instance of Bio::DB::HTS::VCF.
"header"
Returns instance of Bio::DB::HTS::VCF::Header, representing the header of the file.
$header = $vcf->header()
"num_variants"
Returns the number of variants (i.e. rows) of the file.
$nv = $vcf->num_variants();
"close"
Close the VCF/BCF file, allocated memory will be released, included the index, if present.
$vcf->close()
"next"
Returns the next row (starting from the first one) read from the file.
$row = $vcf->next()
Returns an instance of Bio::DB::HTS::VCF::Row or undef if end of file is reached.
Querying an indexed VCF/BCF file
If the file is indexed, the file can be queried for variants on a specified region.
Regions can be specified using either the "chr", "chr:start" or "chr:start-end" format,
with start <= end.
Once an iterator is obtained, individual rows belonging to the result set can be
sequentially accessed by iteratively invoking the iterator next method until it returns
nothing.
"query"
$iterator = $vcf->query($region);
Returns an instance of Bio::DB::HTS::VCF::Iterator or undef if the chromosome is not
found in the index or raises an exception in case the underlying HTSlib library cannot
parse the region.
HEADER METHODS
Once the file has been opened, various global values can be read from the header.
"version"
Returns the VCF file version, as a string
$h->version()
"num_samples"
Returns the number of samples
$h->num_samples()
"get_sample_names"
Returns the list of sample names
$sample_names = $h->get_sample_names()
Returns an array ref of strings representing the sample names
"get_seqnames"
Returns the number of sequence names
$h->num_seqnames()
"get_seqnames"
Returns the list of sequence names
$h->get_seqnames()
Returns an array ref of strings representing the sequence names
"fmt_text"
Get header formatted text, as a string
$h->fmt_text()
Returns the text string representing the content of the header
ROW METHODS
Individual rows can be read in and fields accessed. To read a row use the next function,
which returns a Bio::DB::HTS::VCF::Row instance.
Various fields can then be read from the row object. Some of the functions to read these
fields will need the header object supplied.
$row->print($header)
Returns a formatted textual representation of the row.
$row->chromosome($header)
$row->position()
$row->id()
$row->quality()
$row->reference()
Accessing alleles information
$row->num_alleles()
Returns the number of alleles
$row->get_alleles()
Returns the alleles as strings in an array ref
The variant type of an allele can be determined using the index of the allele. The index
starts from 1 for the first allele:
$row->is_snp()
Returns a true value if the row refers to a SNP.
$row->get_variant_type($allele_index)
This will return one of the values as defined in htslib. As of v1.3.1 these are as
follows.
VCF_REF 0
VCF_SNP 1
VCF_MNP 2
VCF_INDEL 4
VCF_OTHER 8
Row filters
Each row object has filters that may or may not have been applied to it.
$row->num_filters()
Returns the number of filters of the row.
$row->has_filter($header, $filter)
Returns 0 if the filter is not present, 1 if it is present. The PASS filter is
represented by a dot.
Accessing info fields
Each row may have additional info fields associated with each allele in the row.
$row->get_info_type($header, $info_id)
Returns the type of the info ID as specified in the VCF file header, one of "String",
"Integer", "Float" or "Flag".
$row->get_info($header, $info_id) or $row->get_info($header)
If an info_id string is passed, returns an array ref of values for that particular info
field, one for each allele in the row. If the row does not have an item of that info, or
it does not exist in the file, a string "ID_NOT_FOUND" will be returned.
Alternatively, the get_info() method can be invoked by just passing the header. In this
case, the whole info field is returned organised as a hash ref where keys are the info
IDs and values are the info fields for the corresponding ID.
Accessing format fields
Formats are dealt with similarly to info fields.
$row->get_format_type($header, $format_id)
Returns the type of the format ID as specified in the VCF file header, one of "String",
"Integer", "Float" or "Flag".
$row->get_format($header, $format_id) or $row->get_format($header)
If a format_id string is passed, returns an array ref of values for that particular
format ID. If the row does not have an item of that format, or it does not exist in the
file, a string "ID_NOT_FOUND" will be returned.
Alternatively, the get_format() method can be invoked by just passing the header. In
this case, it returns the complete format specification as a hash ref of FORMAT_ID => [
FORMAT_ID_VALUE, ... ].
Accessing genotypes
Genotype records are currently returned as a series of integers, across all the samples
for the row.
$row->get_genotypes($header)
Returns an array reference of integers representing genotype records.
VCF SWEEP OBJECTS
Open the file and process using sweeps. Note that the two methods maintain pointers that
are independant of one another. Using the next_row() will start at the first row in the
file and go on to the next row in subsequent reads. This is independant of previous_row()
calls. Similarly previous_row() will start at the last row and read backwards. However a
call to next_row() is needed beforehand as the read fails otherwise.
At the time of writing there are issues which seem to be due to the underlying HTSlib API
calls, so using the next() function is preferable to using sweeps.
use Bio::DB::HTS::VCF ;
my $sweep = Bio::DB::HTS::VCFSweep->new(filename => "data/test.vcf.gz");
$sweep->header;
my $row_forwards = $sweep->next_row(); #returns first row in file
my $row_backwards = $sweep->previous_row(); #returns last row in file
my $row_forwards = $sweep->next_row(); # returns second row in file
my $row_backwards = $sweep->previous_row(); #returns penultimate row in file