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VcfCodingSnps

19 bytes added, 02:20, 20 September 2010
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-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 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
-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
1. Gene file used should be of [http://genome.ucsc.edu/FAQ/FAQformat#format9 GenePred table format]. The following 11 10 fields are required and must be of the same order as shown below:
string name; "Name of gene"
string chrom; "Chromosome name"
uint[exonCount] exonStarts; "Exon start positions"
uint[exonCount] exonEnds; "Exon end positions"
2.
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).
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