Visualizing Vcf Files With Igv

Question

[GPR]

Hello, I have generated vcf files using VarScan v2.3.2 and am trying to visualize them in IGV. I have indexed the files with either IGV-tools or tabix, followed by bgzip in both cases. When I upload one of these files in IGV, it appears as if 2 tracks are present (the reference track and the vcf track), but I can only see the transcript reference one. I tried changing the track height and expanding the tracks with no success. Can somebody comment on what's the catch with this? Thanks, G.

[brentp]

hopefully you mean you ran bgzip and then indexed with tabix

Answer 1

[samsara]

You should be able to visualize VCF file in IGV if you have index file for corresponding VCF file. My assumption is, there must be something wrong with yor VCF file.

I have visualized reference genome, BAM file and VCF file that contains SNP called from the same BAM file. When I zoom the view to the fullest and go to the region of one of SNPs ( I looked into my VCF file and picked one SNP location) I can clearly see my SNP of interest.