VCF-ISEC(1) User Commands VCF-ISEC(1)NAME
vcf-isec - create intersections, unions, complements on bgzipped and tabix indexed VCF or tab-delimited files
SYNOPSIS
vcf-isec [OPTIONS] file1.vcf file2.vcf ...
DESCRIPTION
About: Create intersections, unions, complements on bgzipped and tabix indexed VCF or tab-delimited files.
Note that lines from all files can be intermixed together on the output, which can yield unexpected results.
OPTIONS -C, --chromosomes <list|file>
Process the given chromosomes (comma-separated list or one chromosome per line in a file).
-c, --complement
Output positions present in the first file but missing from the other files.
-d, --debug
Debugging information
-f, --force
Continue even if the script complains about differing columns.
-o, --one-file-only
Print only entries from the left-most file. Without -o, all unique positions will be printed.
-n, --nfiles [+-=]<int>
Output positions present in this many (=), this many or more (+), or this many or fewer (-) files.
-p, --prefix <path>
If present, multiple files will be created with all possible isec combinations. (Suitable for Venn Diagram analysis.)
-t, --tab <chr:pos:file>
Tab-delimited file with indexes of chromosome and position columns. (1-based indexes)
-w, --win <int>
In repetitive sequences, the same indel can be called at different positions. Consider records this far apart as matching (be it a
SNP or an indel).
-h, -?, --help
This help message.
EXAMPLES
bgzip file.vcf; tabix -p vcf file.vcf.gz bgzip file.tab; tabix -s 1 -b 2 -e 2 file.tab.gz
vcf-isec 0.1.5 July 2011 VCF-ISEC(1)
Check Out this Related Man Page
pycocuma(1) Addressbook pycocuma(1)NAME
pycocuma - Pythonic Contact and Customer Management
SYNTAX
pycocuma [options] [connection-string]
DESCRIPTION
PyCoCuMa (Pythonic Contact and Customer Management) provides a personal information system for addresses, telephone numbers and other data
associated with personal contacts (also supports photographic pictures).
PyCoCuMa is purely written in Python with a Tk graphical interface. PyCoCuMa is based on an XML-RPC client-server architecture. The server
stores its data in compatible vCard (ver. 3.0) files (*.vcf) which can be read by all modern address programs (Evolution, KAddressbook,
Outlook, GnomeCard, etc).
This manpage documents the PyCoCuMa client (which can also run standalone).
OPTIONS
connection-string
addressbook filename / server url
-h --help
show help
-c --config
location of configuration file (default: ~/.pycocuma)
--noconf
do not save configuration / preferences
-t --type
connection type: xmlrpc or file (default: file)
--finder
open QuickFinder
--import
import from file/stdin (-) (e.g. vcard:/tmp/John.vcf)
--export
export to file or stdout (e.g. latex:-)
EXAMPLES
pycocuma --type=xmlrpc http://localhost:8810
pycocuma --config=/tmp/pycocumatest.conf --type=file ./addressbook.vcf
AUTHORS
PyCoCuMa was written by Henning Jacobs.
This manpage was written by Christoph Berg for the Debian GNU/Linux distribution (but may be used by others).
SEE ALSO
PyCoCuMa home page
http://www.srcco.de/pycocuma/
pycocuma-server(1)Debian 0.4.5-5 pycocuma(1)
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