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how to visulize structure variants

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!

variant igv bam structral
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updated by Medhat Medhat • written by gaom001 • gaom001

1 answer

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

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written by Medhat Medhat

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.

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written by gaom001 • gaom001

Great!! Samplot is your friend plus IGV.

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written by Medhat Medhat

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