.Genome Files For Igv For Human_G1K_V37

Question

[Cbio]

One can change the genome loaded in IGV. To see the gene annotations, IGV needs an annotation file. I want to load 1000 genomes hg 37. But where's its gene file?

Answer 1

[Vikas Bansal]

I think it is already included in igv and you can select hg19 or 37. But I found this post similar to your question and Jim (first author of igv paper) and pmiguel have covered the problems. Some suggestions from the post-

You have to either get the chromosomes names in your .bam file(s) to match those in the hg19 genome annotation, or create an alias file.

For creating alias file, details are here

Basically, the problem is because of chromosome names in your file and genome file. So if you will make sure that names are same (or you can create alias file), then everything will be fine.