SortVCFOnRef

#WARNING

I've moved SortVCFOnRef to SortVCFOnRef2 the new command line is now:

##Motivation

Sort a VCF using the order defined by the indexed Reference genome.

##Compilation

see also Compilation

ant sortvcfonref2

##Synopsis

$ java -cp  -jar dist/sortvcfonref2.jar [options] (stdin|file.vcf)

##Options

 -R (fasta) indexed reference. Optional. The order of this reference will be used for sorting
 -T (dir) add tmp directory (optional)
 -N (int) max records in ram. default: 50000
 -h get help (this screen)
 -v print version and exit.
 -L (level) log level. One of java.util.logging.Level . currently:null

##Example

cat input.vcf |\
   java -jar dist/sortvcfonref2.jar  -R ref.fa |\
   bgzip -c > result.vcf.gz && \
   tabix -p vcf -f result.vcf.gz