VcfCodingSnps
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vcfCodingSnps 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.
Basic Usage Example
Here is an example of how vcfCodingSnps works:
vcfCodingSnps -s chrom22-CHB.vcf -g genelist.txt -o annotated-chrom22-CHB.vcf
Command Line Options
-s SNP file Specifies the name of the input VCF-format SNP file -g genefile Specifies the name of the input gene file, by default use gene list file in ASCII format generated by UCSC genome browser -o output file Specifies the name of the output VCF-format SNP file
Input File Infomation
1. Example headlines of input VCF-format SNP file:
##format=VCFv3.2 ##NA12891=../depthFilter/filtered.NA12891.chrom22.SLX.maq.SRP000032.2009_07.glf ##NA12892=../depthFilter/filtered.NA12892.chrom22.SLX.maq.SRP000032.2009_07.glf ##NA12878=../merged/NA12878.chrom22.merged.glf ##minTotalDepth=0 ##maxTotalDepth=1000 ##minMapQuality=30 ##minPosterior=0.9990 ##program=glfTrio ##versionDate=Tue Dec 1 00:42:24 2009 #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA12891 NA12892 NA12878 22 14439753 . a t 100 mapQ=0 depth=68;duples=homs;mac=2 GT:GQ:DP 1|1:100:40 0|0:81:28 1|0:84:0 22 14441250 . t c 59 mapQ=0 depth=40 GT:GQ:DP 1|1:56:25 1|1:31:15 1|1:32:0 22 14443154 . t g 45 mapQ=9 depth=92;duples=homs;mac=2 GT:GQ:DP 1|1:49:21 0|0:60:20 1|0:100:51 ... ...
2. Input gene file should be a plain text file generated by ucsc genome browser. A sample pathway of generating an input gene file is
Go to http://genome.ucsc.edu/ ►► Click "table" ►► Specify the fields required (clade: mammal, genome:human etc.) ►► get output gene file 1. A detailed instruction on using the table browser could be found at genome.ucsc.edu/cgi-bin/hgTables
