Question: CNV caller software
0
gravatar for Bogdan
20 months ago by
Bogdan480
Palo Alto, CA, USA
Bogdan480 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 • 1.5k views
ADD COMMENTlink modified 20 months ago by Lemire/OICR350 • written 20 months ago by Bogdan480
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 20 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 20 months ago by Bogdan480
1
gravatar for Eric T.
20 months ago by
Eric T.2.1k
San Francisco, CA
Eric T.2.1k wrote:

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

ADD COMMENTlink written 20 months ago by Eric T.2.1k
1
gravatar for EagleEye
20 months ago by
EagleEye5.1k
Sweden
EagleEye5.1k wrote:

For array,

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

ADD COMMENTlink written 20 months ago by EagleEye5.1k
1
gravatar for chloe.steen
20 months ago by
chloe.steen130
Oslo
chloe.steen130 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 20 months ago by chloe.steen130
1
gravatar for Jeffin Rockey
20 months ago by
Jeffin Rockey480
Karimannoor
Jeffin Rockey480 wrote:

Please see cn.MOPS also.

Jf

ADD COMMENTlink written 20 months ago by Jeffin Rockey480
1
gravatar for ssv.bio
20 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 20 months ago • written 20 months ago by ssv.bio170
0
gravatar for Bogdan
20 months ago by
Bogdan480
Palo Alto, CA, USA
Bogdan480 wrote:

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

ADD COMMENTlink written 20 months ago by Bogdan480
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