public final class Jannovar extends Object
TranscriptModel
objects and to serialize them. The resulting serialized file can be used both
by this program itself (see next item) or by the main Exomizer program to annotated VCF file.
TranscriptModel
objects (see above item) annotate a VCF file using
annovar-type program logic. Note that this functionality is also used by the main Exomizer program and thus this
program can be used as a stand-alone annotator ("Jannovar") or as a way of testing the code for the Exomizer.
To run the "Jannovar" executable:
java -Xms1G -Xmx1G -jar Jannovar.jar -V xyz.vcf -D $SERIAL
This will annotate a VCF file. The results of de.charite.compbio.jannovar annotation are shown in the form
Annotation {original VCF line}
Just a reminder, to set up annovar to do this, use the following commands.
perl annotate_variation.pl --downdb knownGene --buildver hg19 humandb/then, to annotate a VCF file called BLA.vcf, we first need to convert it to Annovar input format and run the main annovar program as follows.
$ perl convert2annovar.pl BLA.vcf -format vcf4 > BLA.av $ perl annotate_variation.pl -buildver hg19 --geneanno BLA.av --dbtype knowngene humandb/This will create two files with all variants and a special file with exonic variants.
There are three ways of using this program.
anno.serialize()
is true and a file ucsc.ser
is created.
Constructor and Description |
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Jannovar() |
public static void main(String[] argv)
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