how to visulize structure variants

Question

[gaom001]

Hi, Community, I am working on SV calling recently, and got vcf file for SV calling. I was wonder how to visulize these SV from the caller. Can I visulize the SV in IGV by using BAM file?

Thanks in advance!

Answer 1

[Medhat]

Are you using long- or short-reads?
Samplot is a good start: https://github.com/ryanlayer/samplot

Additionally, you can use IGV with BAM and indexed VCF file, it will help you to visualize Deletions (DEL) and Insertions (INS). Lastly, this is a nice review for other tools and when to use it https://www.nature.com/articles/s10038-019-0687-0

[gaom001]

Hi Medhat, I used the short reads (~150 bp ). Thanks for the info, I will test them and let you know if I have more questions. Thanks again.

[Medhat]

Great!! Samplot is your friend plus IGV.