Question: visualize CNV data based on WGS
1
gravatar for Bogdan
4 months ago by
Bogdan480
Palo Alto, CA, USA
Bogdan480 wrote:

Dear all,

we have been calling CNV (copy-number variations) in cancer genomes based on whole-genome sequencing data (WGS). Please would you advise -- what would be the best way to visualize WGS in order inspect visually the CNV predictions ?
The BAM files of germline and tumor samples are big (> 60-80 GB).

thanks a lot !

-- bogdan

cnv • 468 views
ADD COMMENTlink modified 3 months ago by Eric T.2.1k • written 4 months ago by Bogdan480
1

Did you tried using terminal genome viewer like https://github.com/dariober/ASCIIGenome maybe it will help.

ADD REPLYlink modified 4 months ago • written 4 months ago by Medhat7.5k

Thank you all for all your comments and suggestions ;)

ADD REPLYlink modified 4 months ago • written 4 months ago by Bogdan480
1

I would like to suggest to keep this gender neutral.

Please use ADD COMMENT or ADD REPLY to answer to previous reactions, as such this thread remains logically structured and easy to follow. I have now moved your post but as you can see it's not optimal. Adding an answer should only be used for providing a solution to the question asked.

If an answer was helpful you should upvote it, if the answer resolved your question you should mark it as accepted. Upvote|Bookmark|Accept

ADD REPLYlink written 4 months ago by WouterDeCoster28k

thank you Wouter for your recommendations.

ADD REPLYlink written 4 months ago by Bogdan480
2
gravatar for Pierre Lindenbaum
4 months ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum107k wrote:

I've written : http://lindenb.github.io/jvarkit/LowResBam2Raster.html , you're just limited by the memory...

it works for my needs, e.g:

ADD COMMENTlink written 4 months ago by Pierre Lindenbaum107k
1
gravatar for Leandro Lima
4 months ago by
Leandro Lima890
San Francisco, CA
Leandro Lima890 wrote:

Hi, Bogdan.

Have you tried IGV? You can load the BAMs and the BED files to check.

Leandro

ADD COMMENTlink written 4 months ago by Leandro Lima890

yes, however we encountered a bit of problem with IGV : when zooming-out, the BAM tracks were not visible anymore in IGV.

ADD REPLYlink written 4 months ago by Bogdan480
1
gravatar for Eric T.
3 months ago by
Eric T.2.1k
San Francisco, CA
Eric T.2.1k wrote:

You can generate a multi-page PDF of scatter plots focused on individual genomic regions (genes, chromosomes, etc.) with cnvkit.py scatter --range-list.

At UCSF you might be able to get access to the group license for Biodiscovery Nexus Copy Number, which is commonly used by pathologists for reviewing array CGH data. You can export CNVkit .cnr files to that program's format with the cnvkit.py export nexus-basic command, or include SNP allele frequencies from a VCF file with export nexus-ogt.

ADD COMMENTlink modified 3 months ago • written 3 months ago by Eric T.2.1k

Dear Eric, thank you very much for your suggestions !

ADD REPLYlink written 3 months ago by Bogdan480
0
gravatar for Nandini
4 months ago by
Nandini550
London
Nandini550 wrote:

You can try Alamut We use it and it works quite well for large BAM files.

ADD COMMENTlink written 4 months ago by Nandini550
0
gravatar for dariober
4 months ago by
dariober9.1k
Glasgow - UK
dariober9.1k wrote:

Thanks to @Medhat for "promoting" my tool. However, also ASCIIGenome and any interactive tool working directly with BAM files will be slow when handling very large regions like CNVs (I have to check out Pierre's solution though!). In my opinion, best option is to convert BAM to bigWig or tdf and work with these instead. Have a look at deepTools (for BAM -> bigWig) and igvtools for BAM to tdf.

ADD COMMENTlink written 4 months ago by dariober9.1k

It would be great If you could implement method to go directly to specific region in genome.

ADD REPLYlink written 4 months ago by Medhat7.5k

Hi- I think this is already available with the -r/--region option. To go directly to chr:start-end:

ASCIIGenome -r chr7:1000-2000 aln.bam

Is this what you mean? (By the way, ASCIIGenome, like IGV, will intentionally not show BAM tracks for very large regions).

ADD REPLYlink written 4 months ago by dariober9.1k

This is what I mean, My bad :)

ADD REPLYlink written 4 months ago by Medhat7.5k

No Worries- feel free to post questions, suggestions, bugs, whatever!

ADD REPLYlink written 4 months ago by dariober9.1k
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