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Displaying structural variants with JBrowse

JBrowse supports GFF3, BED, FASTA, Wiggle, BigWig, BAM, VCF (with tabix), REST, and more file formats.

If we can call large structural variants and record these calls in one of the file formats listed above, then in theory we should be able to display them via JBrowse.

Can anyone recommend how to call large structural variants, record the calls in one of the file formats listed above, and display them via JBrowse?

(Large structural variants are things such as large INDELs, translocations, chromosomal inversions, etc.)

Thank you.

jbrowse genome visualization
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written by joneill4x joneill4x

2 answers

JBrowse should be ok with displaying structural variants encoded in VCFTabix.

Structural variants in VCF are generally written by having something like <del> in the ALT field, the start column is just the start of the feature and the END=123456 in the INFO field indicates the end of the feature. The interchromosomal translocations are a little more complicated using something call the breakend spec, which takes a little getting used to. Either way, jbrowse can at least display these

Also as a brief side note, we are currently developing JBrowse 2 which is aimed at displaying structural variation even better, for example by displaying two chromosomes at once, and drawing the interchromosomal connections. We aim to have a preview available soon, if you're interested let me know

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written by cmdcolin cmdcolin

I am very interested. Please let me know how I can get involved.

I guess that means I should hurry up and figure out how to call the structural variants and store them in a VCF!

Thanks cmdcolin.

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written by joneill4x joneill4x

I will send you a link to a signup form soon regarding this

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written by cmdcolin cmdcolin

Hi joneill4x (and anyone else reading this) If you are interested here is a signup link for our JBrowse "early access program" http://jbrowse.org/eap

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written by cmdcolin cmdcolin

I used Manta and paftools to call structural variants and store them in a VCF format, which was displayed in JBrowse.

For Manta, I had to filter the VCF file to keep only variants with 'PASS'.

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written by joneill4x joneill4x

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