Question: CNV caller software
0
gravatar for Bogdan
15 months ago by
Bogdan320
Palo Alto, CA, USA
Bogdan320 wrote:

Dear all,

any suggestions regarding a good algorithm to use to call CNV (copy number variants) in the cancer genomes ? many thanks !

-- bogdan

cnv • 1.1k views
ADD COMMENTlink modified 14 months ago by Lemire/OICR350 • written 15 months ago by Bogdan320
2

Do you need a CNV caller for whole genome sequencing data? Or exome sequencing data?

Do you have a paired normal sample to compare with? Or just a tumor sample?

ADD REPLYlink written 14 months ago by Jared Evans80

Thank you Jared. We would need a CNV caller on WGS data, we do have paired normal-tumor samples, and any suggestions would be welcome. Many thanks !

ADD REPLYlink written 14 months ago by Bogdan320
1
gravatar for Eric T.
15 months ago by
Eric T.1.9k
San Francisco, CA
Eric T.1.9k wrote:

At UCSF's cancer genome sequencing service we've been using CNVkit with good results.

ADD COMMENTlink written 15 months ago by Eric T.1.9k
1
gravatar for EagleEye
15 months ago by
EagleEye4.8k
Sweden
EagleEye4.8k wrote:

For array,

http://penncnv.openbioinformatics.org/en/latest/

ADD COMMENTlink written 15 months ago by EagleEye4.8k
1
gravatar for chloe.steen
14 months ago by
chloe.steen120
Oslo
chloe.steen120 wrote:

ASCAT, FACETS, Theta, ABSOLUTE, ADTex, CopyCat, copynumber, depending on the type of data you have.

I personally use ASCAT for array data, and it has been used in several articles as the gold standard to compare tools, and FACETS for exome sequencing, it was published this summer, and my first impression is quite good.

ADD COMMENTlink written 14 months ago by chloe.steen120
1
gravatar for Jeffin Rockey
14 months ago by
Jeffin Rockey410
Jeffin Rockey410 wrote:

Please see cn.MOPS also.

Jf

ADD COMMENTlink written 14 months ago by Jeffin Rockey410
1
gravatar for ssv.bio
14 months ago by
ssv.bio170
ssv.bio170 wrote:

GISTIC (http://portals.broadinstitute.org/cgi-bin/cancer/publications/pub_paper.cgi?mode=view&paper_id=216&p=t), DNAcopy (https://bioconductor.org/packages/release/bioc/html/DNAcopy.html)

ADD COMMENTlink modified 14 months ago • written 14 months ago by ssv.bio170
0
gravatar for Bogdan
14 months ago by
Bogdan320
Palo Alto, CA, USA
Bogdan320 wrote:

Thank you all for suggestions ! Has anyone experience with HMMcopy and TITAN ? how well do these tools do ?

ADD COMMENTlink written 14 months ago by Bogdan320
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