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:

  #VCF_test

  #VCF_test

  #from http://www.sph.umich.edu/csg/liyanmin/vcfCodingSnps/Tutorial.shtml

  #from http://csg.sph.umich.edu//liyanmin/vcfCodingSnps/Tutorial.shtml

  #CHROM  POS    ID      REF    ALT    QUAL    FILTER  INFO    FORMAT  NA12891 NA12892 NA12878

  #CHROM  POS    ID      REF    ALT    QUAL    FILTER  INFO    FORMAT  NA12891 NA12892 NA12878

  1      3      .      A      G      50      depth=20        ANNO=GENE1/CODING_GENE:+:Exon:Utr5:Normal_Splice_Site|GENE3/CODING_GENE:-:Exon:Utr3:Normal_Splice_Site|GENE2/NON_CODING_GENE:+:Upstream GT:GQ:GD        1/0:31:12      0/0:28:14

  1      3      .      A      G      50      depth=20        ANNO=GENE1/CODING_GENE:+:Exon:Utr5:Normal_Splice_Site|GENE3/CODING_GENE:-:Exon:Utr3:Normal_Splice_Site|GENE2/NON_CODING_GENE:+:Upstream GT:GQ:GD        1/0:31:12      0/0:28:14

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.