Visualise SNPs with IGV

[boetsie]

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 121 122 A
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

[Rao]

Use GFF3 format