Difference between revisions of "VcfCodingSnps"

From Genome Analysis Wiki
Jump to: navigation, search
Line 10: Line 10:
  
 
   -s ''SNP file''                    Specifies the name of the input [[VCF]]-format SNP file
 
   -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 generated by UCSC genome browser  
+
   -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
 
   -o ''output file''                Specifies the name of the output VCF-format SNP file

Revision as of 14:17, 20 November 2009

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