Changes

   -s SNP file                      Specifies the name of input VCF-format SNP file

   -s SNP file                      Specifies the name of input VCF-format SNP file

   -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

   -g genefile                     Specifies the name of input gene file, by default use a NCBI36 version gene list file (genelist.txt) in UCSC known gene format generated by UCSC genome browser

   -o output file             Specifies the name of output VCF-format SNP file, by default will be named vcfCodingSNP.out.vcf

   -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

   -r reference genome                Specifies the name of reference genome file, by default will use NCBI build 36 reference genome

   Go to http://genome.ucsc.edu/ ►► Click "table" ►► Specify the fields required (clade: mammal, genome:human etc.) ►► In "track" filed, select "UCSC gene" ►► get output gene file

   Go to http://genome.ucsc.edu/ ►► Click "table" ►► Specify the fields required (clade: mammal, genome:human etc.) ►► In "track" filed, select "UCSC gene" ►► get output gene file

   

   

  1. Gene file used should be of [http://genome.ucsc.edu/FAQ/FAQformat#format9 GenePred table format]. The following 11 fields are required and must be of the same order as shown below:

  1. Gene file used should be of [http://genome.ucsc.edu/FAQ/FAQformat#format9 GenePred table format]. The following 10 fields are required and must be of the same order as shown below:

     string  name;              "Name of gene"

     string  name;              "Name of gene"

     string  chrom;              "Chromosome name"

     string  chrom;              "Chromosome name"

     uint[exonCount] exonStarts; "Exon start positions"

     uint[exonCount] exonStarts; "Exon start positions"

     uint[exonCount] exonEnds;  "Exon end positions"

     uint[exonCount] exonEnds;  "Exon end positions"

 

  2. A detailed instruction on using the table browser could be found at [http://genome.ucsc.edu/cgi-bin/hgTables?command=start#Help genome.ucsc.edu/cgi-bin/hgTables].

  2. A detailed instruction on using the table browser could be found at [http://genome.ucsc.edu/cgi-bin/hgTables?command=start#Help genome.ucsc.edu/cgi-bin/hgTables].

  3. One can specify the region to be the whole genome or any particular gene position (e.g. chr21:33031597-33041570).

  3. One can specify the region to be the whole genome or any particular gene position (e.g. chr21:33031597-33041570).