Question: Displaying structural variants with JBrowse
0
gravatar for joneill4x
5 weeks ago by
joneill4x50
Canada
joneill4x50 wrote:

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.

ADD COMMENTlink modified 5 weeks ago by cmdcolin1.3k • written 5 weeks ago by joneill4x50
1
gravatar for cmdcolin
5 weeks ago by
cmdcolin1.3k
United States
cmdcolin1.3k wrote:

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

ADD COMMENTlink written 5 weeks ago by cmdcolin1.3k

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.

ADD REPLYlink written 5 weeks ago by joneill4x50

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

ADD REPLYlink written 4 weeks ago by cmdcolin1.3k

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

ADD REPLYlink written 23 days ago by cmdcolin1.3k
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