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*A reference SNP and flanking region
*A reference SNP and flanking region
<pre> --refsnp <your snp> --flank 500kb </pre>
<pre> --refsnp <your snp> --flank 500kb </pre>
*A reference SNP and chromosome/start/stop specification
*A reference SNP and chromosome/start/stop specification
<pre> --refsnp <your snp> --chr # --start <base position> --end <base position> </pre>
<pre> --refsnp <your snp> --chr # --start <base position> --end <base position> </pre>
*A reference SNP and gene:
<pre> --refsnp <your snp> --refgene <your gene> </pre>
This will use the reference gene as the plotting boundaries. You can extend the boundaries by also including --flank.
*A gene and flanking region
*A gene and flanking region
<pre> --refgene <your gene> --flank 250kb </pre>
<pre> --refgene <your gene> --flank 250kb </pre>
