Question: visualize CNV data based on WGS
1
gravatar for Bogdan
10 months ago by
Bogdan680
Palo Alto, CA, USA
Bogdan680 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 • 891 views
ADD COMMENTlink modified 9 months ago by Eric T.2.3k • written 10 months ago by Bogdan680
1

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

ADD REPLYlink modified 10 months ago • written 10 months ago by Medhat8.0k

Thank you all for all your comments and suggestions ;)

ADD REPLYlink modified 10 months ago • written 10 months ago by Bogdan680
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 10 months ago by WouterDeCoster34k

thank you Wouter for your recommendations.

ADD REPLYlink written 10 months ago by Bogdan680
2
gravatar for Pierre Lindenbaum
10 months ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum114k 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 10 months ago by Pierre Lindenbaum114k
1
gravatar for Leandro Lima
10 months ago by
Leandro Lima900
San Francisco, CA
Leandro Lima900 wrote:

Hi, Bogdan.

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

Leandro

ADD COMMENTlink written 10 months ago by Leandro Lima900

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 10 months ago by Bogdan680
1
gravatar for Eric T.
9 months ago by
Eric T.2.3k
San Francisco, CA
Eric T.2.3k 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 9 months ago • written 9 months ago by Eric T.2.3k

Dear Eric, thank you very much for your suggestions !

ADD REPLYlink written 9 months ago by Bogdan680
0
gravatar for Nandini
10 months ago by
Nandini700
London
Nandini700 wrote:

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

ADD COMMENTlink written 10 months ago by Nandini700
0
gravatar for dariober
10 months ago by
dariober9.7k
Glasgow - UK
dariober9.7k 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 10 months ago by dariober9.7k

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

ADD REPLYlink written 10 months ago by Medhat8.0k

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 10 months ago by dariober9.7k

This is what I mean, My bad :)

ADD REPLYlink written 10 months ago by Medhat8.0k

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

ADD REPLYlink written 10 months ago by dariober9.7k
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