VcfFilterNotInPedigree

##Motivation

Adds a FILTER NotInPedigree if the only not(homref) genotypes are not in a pedigree

##Compilation

java 1.8 http://www.oracle.com/technetwork/java/index.html (NOT the old java 1.7 or 1.6) . Please check that this java is in the ${PATH}. Setting JAVA_HOME is not enough : (e.g: https://github.com/lindenb/jvarkit/issues/23 )
GNU Make > 3.81
curl/wget
git
apache ant is only required to compile htsjdk
xsltproc http://xmlsoft.org/XSLT/xsltproc2.html

$ git clone "https://github.com/lindenb/jvarkit.git"
$ cd jvarkit
$ make vcffilternotinpedigree

by default, the libraries are not included in the jar file, so you shouldn't move them (https://github.com/lindenb/jvarkit/issues/15#issuecomment-140099011 ). You can create a bigger but standalone executable jar by addinging standalone=yes on the command line:

$ git clone "https://github.com/lindenb/jvarkit.git"
$ cd jvarkit
$ make vcffilternotinpedigree standalone=yes

The required libraries will be downloaded and installed in the dist directory.

The a file local.mk can be created edited to override/add some paths.

For example it can be used to set the HTTP proxy:

http.proxy.host=your.host.com
http.proxy.port=124567

##Synopsis

$ java -jar dist/vcffilternotinpedigree.jar  [options] (stdin|file.vcf|file.vcf.gz)

Options

-o|--output (OUTPUT-FILE) Output file. Default:stdout
-f|--filter (VALUE) FILTER name. Will be set for variant where the only genotypes non-homref are NOT in the pedigree Default value : "NoGenotypeInPedigree".
-r|--remove remove the variant instead of setting the FILTER Default value : "false".
-h|--help print help
-version|--version show version and exit

##Source Code