Changes

Required files:

Required files:

* [http://www.sph.umich.edu/csg/zhanxw/software/anno/resources/hs37d5.fa hs37d5.fa] Reference genome in NCBI build 37 (you also need to download [http://www.sph.umich.edu/csg/zhanxw/software/anno/resources/hs37d5.fa.fai hs37d5.fai] )

* [http://csg.sph.umich.edu//zhanxw/software/anno/resources/hs37d5.fa hs37d5.fa] Reference genome in NCBI build 37 (you also need to download [http://csg.sph.umich.edu//zhanxw/software/anno/resources/hs37d5.fa.fai hs37d5.fai] )

* [http://www.sph.umich.edu/csg/zhanxw/software/anno/resources/refFlat_hg19.txt.gz refFlag_hg19.txt.gz] Gene database in refFlat format (from UCSC website). You can also use [http://www.sph.umich.edu/csg/zhanxw/software/anno/resources/refFlat.gencode.v7.gz Gencode version 7] or [http://www.sph.umich.edu/csg/zhanxw/software/anno/resources/refFlat.gencode.v11.gz Gencode version 11].

* [http://csg.sph.umich.edu//zhanxw/software/anno/resources/refFlat_hg19.txt.gz refFlag_hg19.txt.gz] Gene database in refFlat format (from UCSC website). You can also use [http://csg.sph.umich.edu//zhanxw/software/anno/resources/refFlat.gencode.v7.gz Gencode version 7] or [http://csg.sph.umich.edu//zhanxw/software/anno/resources/refFlat.gencode.v11.gz Gencode version 11].

* [http://www.sph.umich.edu/csg/zhanxw/software/anno/codon.txt codon.txt] Human codon table.

* [http://csg.sph.umich.edu//zhanxw/software/anno/codon.txt codon.txt] Human codon table.

* [http://www.sph.umich.edu/csg/zhanxw/software/anno/priority.txt priority.txt] Priority file, which determines wich annotation type is more important

* [http://csg.sph.umich.edu//zhanxw/software/anno/priority.txt priority.txt] Priority file, which determines wich annotation type is more important

Outputs:

Outputs: