<?xml version="1.0"?>
<tool xmlns:date="http://exslt.org/dates-and-times" hidden="false" id="com.github.lindenb.jvarkit.tools.vcftrios.VCFTrios" version="f21676175ed7d18ec569f34973dd2c03c23ab1e9" name="vcftrio">
  <!--Date: 2015-02-27T15:54:05+01:00-->
  <description>Check for mendelian incompatibilities in a VCF</description>
  <requirements>
    <requirement type="binary">java</requirement>
  </requirements>
  <command>(gunzip -c ${input} || cat ${input}) | java -cp  $__tool_directory__/commons-jexl-2.1.1.jar:$__tool_directory__/commons-logging-1.1.1.jar:$__tool_directory__/htsjdk-1.128.jar:$__tool_directory__/snappy-java-1.0.3-rc3.jar:$__tool_directory__/vcftrio.jar com.github.lindenb.jvarkit.tools.vcftrios.VCFTrios $filter -p $ped -o ${output}.vcf.gz &amp;&amp; mv  ${output}.vcf.gz ${output}</command>
  <inputs>
		 <param format="vcf" name="input" type="data" label="VCF input"/> 
		<param name="filter" type="boolean" checked="false" label="Create a FILTER in the FILTER column" truevalue="-f" falsevalue=""/>
		<param name="ped" type="data" format="tabular" label="Pedigree file (Family/name/father/mother/sex)"/>
	</inputs>
  <outputs>
    <data format="vcf" name="output"/>
  </outputs>
  <stdio>
    <exit_code range="1:"/>
    <exit_code range=":-1"/>
  </stdio>
  <help>

**Inputs**


- **VCF input** :  VCF input

- **Create a FILTER in the FILTER column** :  Create a FILTER in the FILTER column

- **Pedigree file (Family/name/father/mother/sex)** :  Pedigree file (Family/name/father/mother/sex)


**Outputs**


- **output** :  output


**Wiki**

https://github.com/lindenb/jvarkit/wiki/VCFTrio

-----


**Author**

Pierre Lindenbaum PhD @yokofakun

**Citation**

If you use this Galaxy tool in work leading to a scientific publication please
cite: Pierre Lindenbaum PhD  https://github.com/lindenb/jvarkit

**Contribute**

- Issue Tracker: http://github.com/lindenb/jvarkit/issues`
- Source Code: http://github.com/lindenb/jvarkit

**License**

The project is licensed under the MIT license.

**Compilation**

Date: 2015-02-27T15:54:05+01:00
Version: f21676175ed7d18ec569f34973dd2c03c23ab1e9
</help>
</tool>