Checking regions with high density of SNPs

Question

[misterie]

Hi,

I calculated number of SNPs in non-overlapping windows in each chromosome. I found regions with extreme numbers of SNPs in compare to other windows. How can I check this region/window? What software can I use to check if this region contain many genes or sth else? I would like do it based on GFF file or sth similar because the same I want to do for windows with no SNPs.

Thank u.

[husensofteng]

this answer might be useful: A: Mapping SNP position to gff file

[gabriel.jabud]

Try using IGV software (https://software.broadinstitute.org/software/igv/download) or if your lab/company will pay for it, Geneious (https://www.geneious.com/). You should be able to visualize the SNPs in IGV once you generate your .genome file (or find it online) and have a VCF file.