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, 02:05, 20 September 2010
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| == Command Line Options == | | == Command Line Options == |
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− | -s ''SNP file'' Specifies the name of the input [[VCF]]-format SNP file | + | -s SNP file Specifies the name of 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 | + | -g genefile Specifies the name of input gene file, by default use a gene list file (genelist.txt) in UCSC known gene 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 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 |
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| == Input File Infomation == | | == Input File Infomation == |