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VcfCodingSnps (view source)

Revision as of 02:05, 20 September 2010

727 bytes added ,  02:05, 20 September 2010
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== Command Line Options  ==
 
== Command Line Options  ==
   −
   -s ''SNP file''                    Specifies the name of the input [[VCF]]-format SNP file
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   -s SNP file                     Specifies the name of input VCF-format SNP file
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   -g ''genefile''                    Specifies the name of the input gene file, by default use gene list file in ASCII format generated by UCSC genome browser  
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   -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
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   -o ''output file''                Specifies the name of the output VCF-format SNP file
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   -o output file             Specifies the name of output VCF-format SNP file, by default will be named vcfCodingSNP.out.vcf
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  -r reference genome                Specifies the name of reference genome file, by default will use NCBI build 36 reference genome
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  -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
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  --n1 parameter             user defined number of bps into intron for splice site, by default will be set to 8
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  --n2 parameter              user defined number of bps into extron for splice site, by default will be set to 3
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  --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  ==
 
== Input File Infomation  ==
Liyanmin
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