Where can I find GV .genome files for igvtools

Question

[Bella_p]

Hi,

I'd like to use igvtools count on the command line. According to the IGV website, it is possible with: "id, or a full path to a .chrom.sizes or an IGV .genome file. " I can't find any IGV .genome file for the command.
I downloaded a zip file containing 3 files:

hg18_cytoBand.txt
hg18_refGene.txt
property.txt

But all text files, without the sequence.
Where can I find the IGV .genome file of hg18 for download?

Answer 1

[dariober]

Just to demystify the "genome file"... This is just a tab-separated table with one row per chromosome giving chromosome name and size like chr1 247249719 (I don't remember if the file name has to end with .chrom.sizes). So it is quite simple and you could prepare it by yourself.

For hg18 I think you can run igvtools using the placeholder hg18 instead of the actual file since igvtools ships with some common genome files (look into the directory IGVTools/genomes/).

Finally, you could download chromosome names and sizes from ucsc using mysql as

mysql --user=genome --host=genome-mysql.cse.ucsc.edu -A -e \
"select chrom, size from hg18.chromInfo" > hg18.chrom.sizes

(I don't think IGV cares about the order of the chromosomes in the genome file).

[Bella_p]

I understand, so one of those files I downloaded actually contains what you wrote. Thanks a lot!

Answer 2

[GenoMax]

The genome file should be in the directory specified under View --> Preferences --> Cram --> Cache Directory.

hg18 genome can be downloaded by going to "Genomes" in GUI window --> More --> Genomes to Add to list --> Selecting hg18 there.