= Annotation from SeattleSeq AnnotationTool =
Annotate Files with Variants through Seattle Seq Annotation: http://gvs.gs.washington.edu/SeattleSeqAnnotation/ . The java code that wraps the forms is provided from SeattleSeq Annotation: http://gvs.gs.washington.edu/SeattleSeqAnnotation/SubmitSeattleSeqAnnotationAutoJob.java . This method wraps the wrapper(..) and provides a python implementation. In order to run there should be a directory under the current path, named "jars" with the following jar files:
 * httpunit.jar
 * js-1.6R5.jar
 * junit-3.8.1.jar
 * nekohtml-0.9.5.jar
 * xercesImpl-2.6.1.jar

= Pipeline Elements =

This section will describe all parts of our annotation pipeline, the scripts have, and the features it will return.

||'''script'''||'''feature'''||'''description'''||'''source'''||
||1KGannotation.py||alleleFreq||allele freq in 1KG||1KG||
||TODO||||||||
||||||||||

= End of Pipeline =

= Related work =

* http://www.svaproject.org/
* http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1001074