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TabAnno

27 bytes removed, 11:57, 2 February 2017
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Required files:
* [http://wwwcsg.sph.umich.edu/csg/zhanxw/software/anno/resources/hs37d5.fa hs37d5.fa] Reference genome in NCBI build 37 (you also need to download [http://wwwcsg.sph.umich.edu/csg/zhanxw/software/anno/resources/hs37d5.fa.fai hs37d5.fai] )
* [http://wwwcsg.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://wwwcsg.sph.umich.edu/csg/zhanxw/software/anno/resources/refFlat.gencode.v7.gz Gencode version 7] or [http://wwwcsg.sph.umich.edu/csg/zhanxw/software/anno/resources/refFlat.gencode.v11.gz Gencode version 11].
* [http://wwwcsg.sph.umich.edu/csg/zhanxw/software/anno/codon.txt codon.txt] Human codon table.
* [http://wwwcsg.sph.umich.edu/csg/zhanxw/software/anno/priority.txt priority.txt] Priority file, which determines wich annotation type is more important
Outputs:
#VCF_test
#from http://wwwcsg.sph.umich.edu/csg/liyanmin/vcfCodingSnps/Tutorial.shtml
#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
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://wwwcsg.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.
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