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, 11:57, 2 February 2017
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| Required files: | | Required files: |
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− | * [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] ) |
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− | * [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]. |
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− | * [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. |
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− | * [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 |
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| Outputs: | | Outputs: |
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| 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]) |
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− | 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. |