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Old 01-21-2011, 01:11 AM   #1
Senior Member
Location: NL, Leiden

Join Date: Feb 2010
Posts: 245
Default Visualise SNPs with IGV

Hi Jim,

I'm currently testing IGV for visualising SNPs on a bacterial genome. I've generated a SNP table with CLC which looks like this;

Reference Position Consensus Position Variation Type Length Reference Variants Allele Variations Frequencies Counts
122 122 SNP 1 G 1 A 100 133
1411 1411 SNP 1 T 1 C 100 135
1639 1639 SNP 1 G 1 A 100 127
1738 1738 SNP 1 A 1 G 100 118

I have converted this file to a simple .bed file;

GENOMENAME 1410 1411 C
GENOMENAME 1638 1639 A
GENOMENAME 1737 1738 G

This all works, as i can read in the file and visualize it along the genome. However, i want to add more information, like the 'Frequences' and 'Counts' column. These columns should be displayed if i scroll over a SNP.

How can i do this? How should the input look like?

Thanks for the help,

boetsie is offline   Reply With Quote
Old 01-21-2011, 03:11 AM   #2
Location: India

Join Date: Oct 2008
Posts: 36

Use GFF3 format
Rao is offline   Reply With Quote

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