VcfFilterNotInPedigree

##Motivation

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

##Compilation

Requirements / Dependencies

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

Download and Compile

$ 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.

edit 'local.mk' (optional)

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)

VCF Concatenation

This tool supports concatenated VCF on input. For each VCf on input, a VCF will be printed in the output. If there is more than one VCF on input, the output will be NOT a valid VCF but a file containing concatenated VCFs.

$ gunzip -c f1.vcf.gz f2.vcf.gz f3.vcf.gz |\
	java -jar dist/vcffilternotinpedigree.jar > out_3_vcfs.txt

If the filename is defined and ends with '.zip': each output VCF will be stored into one zip entry.

$ gunzip -c f1.vcf.gz f2.vcf.gz f3.vcf.gz |\
	java -jar dist/vcffilternotinpedigree.jar -o result.zip

Options

-o|--output (OUTPUT-FILE) Output file. Default:stdout. This tool supports concatenated VCF on input. For each VCf on input, a VCF will be printed in the output. If the filename is defined and ends with 'zip'. Each output VCF will be stored into one zip entry.
-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".
-s|--singleton (VALUE) Variant is flagged/FILTERed as SingletonAlt if the ALT if found in less or equal times 'singleton-times' in the genotypes Default value : "1".
-sf|--sfilter (VALUE) FILTER name for option singleton Default value : "SingletonAlt".
-h|--help print help
-version|--version show version and exit

##Source Code

Main code is: https://github.com/lindenb/jvarkit/blob/master/src/main/java/com/github/lindenb/jvarkit/tools/burden/VcfFilterNotInPedigree.java