Question: Structural Variant Visualisation from VCF source.
0
gravatar for morovatunc
3.1 years ago by
morovatunc400
Turkey
morovatunc400 wrote:

Hello,

My question is not a straight forward how to plot a circos plot of structural rearrangement data. I have checked more than 2 threads about this topic

Which program, tool, or strategy do you use to visualize genomic rearrangements? How To Visualize Gene Fusions To Better Illustrate The Gene Structure?

But nearly all of the algorithms were based on the bam input. My problem is different than the common questions. I have obtained ~250 patient's ( Prostate Cancer) mutation files from ICGC. (vcfs for SNV,INDEL and structural variants). My aim is to get, TMPRSS2:ERG fusion positive/negative information from these vcfs. Since all the methods require a bam file, I simply thing there must be a way to get this information without downloading vcfs.

So I would be glad if you could answer the following;

Is there a way to scan this without visualising and checking by eye. —> I wanted to see by eye because for some patients, there are deletions in TMPRSS2 and ERG and I thought may be it is a low quality translocation therefore annotated as deletion.

I also have a bedpe format data, if there is a way related with this data format, I can also give it a shot.

Any help would really be appreciated. I have been working for this a quite long time so please forgive my frustration.

Best regards,

Tunc.

rna-seq circos vcf • 1.4k views
ADD COMMENTlink modified 3.1 years ago • written 3.1 years ago by morovatunc400

Hi Tunc,

You may have figured out that I am no longer working at the ICGC DCC #sadface. Are you still posting questions to their dcc-support Help desk? Anybody answering you? I have never used the circos plotting software but it looks cool. If you have other questions that I might be able to answer please feel free to contact me. I have started working on a Prostate Cancer project based at UCSF.

-- Marc Perry

ADD REPLYlink written 3.1 years ago by Marc Perry50
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