Difference between revisions of "VcfCodingSnps"
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-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
