VCFFixIndels

Motivation

Fix samtools INDELS for @SolenaLS

Compilation

See also Compilation

$ make vcffixindels

Options

Option	Description
-o (filename)	filename out. Default: stdout
-h	get help (this screen) and exit.
-v	print version and exit.
-L (level)	log level. One of java.util.logging.Level . Optional.

Example

$ java -jar dist/vcffixindels.jar input.vcf.gz | grep FIX

2	749862	.	T	TT	94.50	.	AC1=2;AF1=1;DP=13;DP4=0,0,5,8;FQ=-73.5;INDEL;INDELFIXED=CTTTTTT|CTTTTTTT|74954856;IS=13,1.000000;MQ=50;VDB=4.019414e-04	GT:PL:DP:GQ	1/1:135,39,0:13:75

See also

• "Unified Representation of Genetic Variants" http://bioinformatics.oxfordjournals.org/content/early/2015/02/19/bioinformatics.btv112.abstract (hey ! it was published after I wrote this tool !)
• https://github.com/quinlan-lab/vcftidy/blob/master/vcftidy.py
• http://www.cureffi.org/2014/04/24/converting-genetic-variants-to-their-minimal-representation/

Contribute

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

##History

• 2013 : Creation

License

The project is licensed under the MIT license.