Question: visualize CNV data based on WGS
1
gravatar for Bogdan
5 weeks ago by
Bogdan420
Palo Alto, CA, USA
Bogdan420 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 • 287 views
ADD COMMENTlink modified 28 days ago by Eric T.2.0k • written 5 weeks ago by Bogdan420
1

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

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

Thank you all for all your comments and suggestions ;)

ADD REPLYlink modified 5 weeks ago • written 5 weeks ago by Bogdan420
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 5 weeks ago by WouterDeCoster26k

thank you Wouter for your recommendations.

ADD REPLYlink written 5 weeks ago by Bogdan420
2
gravatar for Pierre Lindenbaum
5 weeks ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum104k 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 5 weeks ago by Pierre Lindenbaum104k
1
gravatar for Leandro Lima
5 weeks ago by
Leandro Lima880
San Francisco, CA
Leandro Lima880 wrote:

Hi, Bogdan.

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

Leandro

ADD COMMENTlink written 5 weeks ago by Leandro Lima880

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 5 weeks ago by Bogdan420
1
gravatar for Eric T.
28 days ago by
Eric T.2.0k
San Francisco, CA
Eric T.2.0k 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 26 days ago • written 28 days ago by Eric T.2.0k

Dear Eric, thank you very much for your suggestions !

ADD REPLYlink written 28 days ago by Bogdan420
0
gravatar for Nandini
5 weeks ago by
Nandini440
UCL, London
Nandini440 wrote:

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

ADD COMMENTlink written 5 weeks ago by Nandini440
0
gravatar for dariober
5 weeks ago by
dariober8.6k
Glasgow - UK
dariober8.6k 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 5 weeks ago by dariober8.6k

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

ADD REPLYlink written 5 weeks ago by Medhat7.4k

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 5 weeks ago by dariober8.6k

This is what I mean, My bad :)

ADD REPLYlink written 5 weeks ago by Medhat7.4k

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

ADD REPLYlink written 5 weeks ago by dariober8.6k
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