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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 chrom1-CHB.vcf -g genelist.txt -o annotated-chrom1-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 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