vcf-annotate(1) [debian man page]

VCF-ANNOTATE(1) 						   User Commands						   VCF-ANNOTATE(1)

NAME

       vcf-annotate - annotate VCF file, add filters or custom annotations

SYNOPSIS

       cat in.vcf | vcf-annotate [OPTIONS] > out.vcf

DESCRIPTION

       About: Annotates VCF file, adding filters or custom annotations. Requires tabix indexed file with annotations.

	      Currently annotates only the INFO column, but it will be extended on demand.

OPTIONS

       -a, --annotations <file.gz>
	      The tabix indexed file with the annotations: CHR	FROM[	TO][	VALUE]+.

       -c, --columns <list>
	      The list of columns in the annotation file, e.g. CHROM,FROM,TO,-,INFO/STR,INFO/GN. The dash in this example indicates that the third
	      column should be ignored. If TO is not present, it is assumed that TO equals to FROM.

       -d, --description <file|string>
	      Header annotation, e.g. key=INFO,ID=HM2,Number=0,Type=Flag,Description='HapMap2 membership'.  The descriptions can be  read  from  a
	      file, one annotation per line.

       -f, --filter <list>
	      Apply filters, list is in the format flt1=value/flt2/flt3=value/etc.

       -h, -?, --help
	      This help message.

   Filters:
       +      Apply all filters with default values (can be overridden, see the example below).

       -X     Exclude the filter X

       1, StrandBias
	      FLOAT		       Min P-value for strand bias (given PV4) [0.0001]

       2, BaseQualBias
	      FLOAT		     Min P-value for baseQ bias [1e-100]

       3, MapQualBias
	      FLOAT		      Min P-value for mapQ bias [0]

       4, EndDistBias
	      FLOAT		      Min P-value for end distance bias [0.0001]

       a, MinAB
	      INT			    Minimum number of alternate bases [2]

       c, SnpCluster
	      INT1,INT2 	       Filters clusters of 'INT1' or more SNPs within a run of 'INT2' bases []

       D, MaxDP
	      INT			    Maximum read depth [10000000]

       d, MinDP
	      INT			    Minimum read depth [2]

       q, MinMQ
	      INT			    Minimum RMS mapping quality for SNPs [10]

       Q, Qual
	      INT			     Minimum value of the QUAL field [10]

       r, RefN
	      Reference base is N []

       W, GapWin
	      INT			   Window size for filtering adjacent gaps [10]

       w, SnpGap
	      INT			   SNP within INT bp around a gap to be filtered [10]

   Example:
	      zcat  in.vcf.gz  |  vcf-annotate	-a  annotations.gz  -d	descriptions.txt  |  bgzip -c >out.vcf.gz zcat in.vcf.gz | vcf-annotate -f
	      +/-a/c=3,10/q=3/d=5/-D -a annotations.gz -d descriptions.txt | bgzip -c >out.vcf.gz

   Where descriptions.txt contains:
	      key=INFO,ID=GN,Number=1,Type=String,Description='Gene Name' key=INFO,ID=STR,Number=1,Type=Integer,Description='Strand'

vcf-annotate 0.1.5						     July 2011							   VCF-ANNOTATE(1)

Text::vCard::Addressbook(3pm)				User Contributed Perl Documentation			     Text::vCard::Addressbook(3pm)

NAME

       Text::vCard::Addressbook - a package to parse, edit and create multiple vCards (RFC 2426)

SYNOPSIS

	 use Text::vCard::Addressbook;

	 my $address_book = Text::vCard::Addressbook->new({
	       'source_file' => '/path/to/address.vcf',
	 });

	 foreach my $vcard ($address_book->vcards()) {
	       print "Got card for " . $vcard->fullname() . "
";
	 }

DESCRIPTION

       This package provides an API to reading / editing and creating multiple vCards. A vCard is an electronic business card. This package has
       been developed based on rfc2426.

       You will find that many applications (Apple Address book, MS Outlook, Evolution etc) can export and import vCards.

READING IN VCARDS

   load()
	 use Text::vCard::Addressbook;

	 # Read in from a list of files
	 my $address_book = Text::vCard::Addressbook->load( ['foo.vCard', 'Addresses.vcf']);

       This method will croak if it is unable to read in any of the files.

   import_data()
	 $address_book->import_data($value);

       This method imports data directly from a string.

   new()
	 # Read in from just one file
	 my $address_book = Text::vCard::Addressbook->new({
	       'source_file' => '/path/to/address.vcf',
	 });

       This method will croak if it is unable to read in the source_file.

	 # File already in a string
	 my $address_book = Text::vCard::Addressbook->new({
	       'source_text' => $source_text,
	 });

	 # Create a new address book
	 my $address_book = Text::vCard::Addressbook->new();

       Looping through all vcards in an address book.

	 foreach my $vcard ($address_book->vcards()) {
	       $vcard->...;
	 }

METHODS

   add_vcard()
	 my $vcard = $address_book->add_vcard();

       This method creates a new empty Text::vCard object, stores it in the address book and return it so you can add data to it.

   vcards()
	 my $vcards = $address_book->vcards();
	 my @vcards = $address_book->vcards();

       This method returns a reference to an array or an array of vcards in this address book. This could be an empty list if there are no entries
       in the address book.

   set_encoding()
	 $address_book->add_vcard('utf-8');

       This method will add the string ';charset=utf-8' to each and every vCard entry. That does help in connection with e.g. an iPhone...

   export()
	 my $vcf_file = $address_book->export()

       This method returns the vcard data in the vcf file format.

       Please note there is no validation, you must ensure that the correct nodes (FN,N,VERSION) are already added to each vcard if you want to
       comply with RFC 2426.

       This might not escape the results correctly at the moment.

AUTHOR

       Leo Lapworth, LLAP@cuckoo.org

COPYRIGHT

       Copyright (c) 2003 Leo Lapworth. All rights reserved.  This program is free software; you can redistribute it and/or modify it under the
       same terms as Perl itself.

ACKNOWLEDGEMENTS

       The authors of Text::vFile::asData for making my life so much easier.

SEE ALSO

       Text::vCard, Text::vCard::Node

perl v5.10.1							    2011-01-11					     Text::vCard::Addressbook(3pm)