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VcfCodingSnps

727 bytes added, 02:05, 20 September 2010
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== 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 a gene list file (genelist.txt) in ASCII UCSC known gene format generated by UCSC genome browser -o ''output file'' Specifies the name of the output VCF-format SNP file, by default will be named vcfCodingSNP.out.vcf -r reference genome Specifies the name of reference genome file, by default will use NCBI build 36 reference genome -l log file Specifies the name of log file, log file gives more detailed information for each annotated SNP, by default will be named vcfCodingSNP.log --n1 parameter user defined number of bps into intron for splice site, by default will be set to 8 --n2 parameter user defined number of bps into extron for splice site, by default will be set to 3 --ns parameter user defined number of kbps for the range of upstream or downstream of a gene, by default will be set t0 5
== Input File Infomation ==
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