how to plot SV(structural variants) from many assemblies of a given locus

Question

[natalev]

How can I visualize structural variants from multiple assemblies of a large locus (for example ~100Mb). Which program can generate a plots similar to this or something like this?

[barslmn]

Try genome browsers/viewers, like IGV, JBrowse or UCSC. You can upload your own data to it. UCSC genome browsers supports custom coloring with the BED format.

[natalev]

Thank you! I was hoping there would be a better way to do this in order to generate good quality figures since looks like it's a common question by now.

[Pierre Lindenbaum]

what is the legend here ? X axis ? y axis ? colors ? red lines ?....

[natalev]

Each row here is assembly of a given locus (~100Mb) in the genome from one human sample. So this is looking at variation across multiple people for a given locus. Different colors represent different structural variants - inversions, duplications , deletions, etc.

[Pierre Lindenbaum]

use circos , ucsc custom tracks ....

[natalev]

Thanks a lot, for your answer!. Circos might not allow simple comparison like in the above figure showing clear structural variation (large deletions ,etc). I will try using UCSC or other viewers to see if I can compress large locus to a figure like above and clearly mark structural variants.