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VcfCodingSnps

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'''vcfCodingSnps'''[http://www.sph.umich.edu/csg/liyanmin/vcfCodingSnps/index.shtml] is a SNP annotation tool that annotates coding variants in a [[VCF]] format input file. It takes a VCF as input and generates an annotated VCF file as output. The tool is currently under development by Yanming Li, a doctoral student at the University of Michigan Center for Statistical Genetics. For any issues with the program, please contact [mailto:liyanmin@umich.edu Yanming]. A detailed tutorial can be found at here [http://www.sph.umich.edu/csg/liyanmin/vcfCodingSnps/index.shtml]
== Basic Usage Example ==
Go to http://genome.ucsc.edu/ ►► Click "table" ►► Specify the fields required (clade: mammal, genome:human etc.) ►► In "track" filed, select "UCSC gene" ►► get output gene file
1. Gene file used should be of [[http://genome.ucsc.edu/FAQ/FAQformat#format9 GenePred table format]]
2. A detailed instruction on using the table browser could be found at [http://genome.ucsc.edu/cgi-bin/hgTables?command=start#Help genome.ucsc.edu/cgi-bin/hgTables].
3. One can specify the region to be the whole genome or any particular gene position (e.g. chr21:33031597-33041570).
The annotating result will be added to the entry "INFO" of the input VCF SNP file and outputted together with other information. If a SNP is annotated differently with respect to different genes (or different isoforms of the same gene), all the annotated results will be added into the entry "INFO". If the SNP is NOT in any gene coding region, then the original "INFO" will be outputted. Here is an example of input and output VCF file headlines:
Input VCF headlines:
##format=VCFv3.2
8 152578 . c t 87 . depth=108 GT:GQ:GD 1/1:95:31 1/1:89:30 1/1:100:47
Output VCF headlines:
##format=VCFv3.2
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