Question: CNV caller software
0
gravatar for Bogdan
9 months ago by
Bogdan250
Palo Alto, CA, USA
Bogdan250 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 • 654 views
ADD COMMENTlink modified 9 months ago by Lemire/OICR350 • written 9 months ago by Bogdan250
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 9 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 9 months ago by Bogdan250
1
gravatar for Eric T.
9 months ago by
Eric T.1.7k
San Francisco, CA
Eric T.1.7k wrote:

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

ADD COMMENTlink written 9 months ago by Eric T.1.7k
1
gravatar for EagleEye
9 months ago by
EagleEye4.1k
Sweden
EagleEye4.1k wrote:

For array,

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

ADD COMMENTlink written 9 months ago by EagleEye4.1k
1
gravatar for chloe.steen
9 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 9 months ago by chloe.steen120
1
gravatar for Jeffin Rockey
9 months ago by
Jeffin Rockey360
Jeffin Rockey360 wrote:

Please see cn.MOPS also.

Jf

ADD COMMENTlink written 9 months ago by Jeffin Rockey360
1
gravatar for ssv.bio
9 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 9 months ago • written 9 months ago by ssv.bio170
0
gravatar for Bogdan
9 months ago by
Bogdan250
Palo Alto, CA, USA
Bogdan250 wrote:

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

ADD COMMENTlink written 9 months ago by Bogdan250
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