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VcfCodingSnps

5 bytes added, 02:38, 20 September 2010
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uint[exonCount] exonEnds; "Exon end positions"
2. If gene file assumes an [http://genome.ucsc.edu/FAQ/FAQformat#format9 extended GenePred format], there will be an exctra "exonframe" field. Please refer to [https://lists.soe.ucsc.edu/pipermail/genome/2006-November/012218.html here] for the definition of "exonframe". For some genes, due to translational frame shifts or other reasons, the exonframe might not
match what one would compute using mod 3 in counting codons. In such cases, the program will report a warning massage that "number of base pairs between code start and code end is not a multiple of three". While we will use the usual mod 3 method for counting codons.  
3. 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].
4. One can specify the region to be the whole genome or any particular gene position (e.g. chr21:33031597-33041570).
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