Snps On Contigs

Question

[jackuser1979]

I see many solutions on visually representing plotting SNPs on chromosome in Biostars. I would like to know how to visually represent plotting SNPs on contigs, any solutions or related paper will be great help.

Answer 1

[Alex Reynolds]

You could upload some custom tracks to the UCSC Genome Browser. You could use BEDOPS conversion scripts to move your data from their native format to BED. Your SNPs could be converted to BED via vcf2bed, and your contigs via bam2bed or sam2bed. You could also try uploading your data as-is, but I don't remember exactly what other formats are supported; the documentation is probably useful, here.