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2. One can specify the regieon to be the whole genome or any particular gene position (e.g. chr21:33031597-33041570).
Here is an example of input gene file headlines:
#name chrom strand txStart txEnd cdsStart cdsEnd exonCount exonStarts exonEnds proteinID alignID
== Output File ==
Some possible annotating results for a single SNP with the meanings of their output format are listed below:
5'UTR=A26C2[-] means the SNP is in the 5'UTR region of gene A26C2 with a minus strand.
STOP_GAINED=MAPK12:Trp49035685stop[-] means that the SNP is at position 49035685 in gene MAPK12 with a minus strand and it changes amino-acid Trp to a stop codon.
The annotating result will be added to the entry "INFO" of the input VCF file and outputted together with other information in the input VCF SNP file. Here is an example of output VCF file headlines: