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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:
Questions and requests should be sent to Xiaowei Zhan ([mailto:zhanxw@umich.edu zhanxw@umich.edu]) or Goncalo Abecasis ([mailto:goncalo@umich.edu goncalo@umich.edu])
Questions and requests should be sent to Xiaowei Zhan ([mailto:zhanxw@umich.edu zhanxw@umich.edu]) or Goncalo Abecasis ([mailto:goncalo@umich.edu goncalo@umich.edu])
Author sincerly appreicate Yanming Li for his wonderful tutorial on gene annotation software [http://www.sph.umich.edu/csg/liyanmin/vcfCodingSnps/Tutorial.shtml vcfCodingSnps], and Hyun Ming Kang for his code related to genome scores and his consistent suggestions and feedbacks.
Author sincerly appreicate Yanming Li for his wonderful tutorial on gene annotation software [http://csg.sph.umich.edu//liyanmin/vcfCodingSnps/Tutorial.shtml vcfCodingSnps], and Hyun Ming Kang for his code related to genome scores and his consistent suggestions and feedbacks.
