Question: CNV caller software
0
gravatar for Bogdan
5 months ago by
Bogdan170
United States
Bogdan170 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 • 425 views
ADD COMMENTlink modified 4 months ago by Lemire/OICR340 • written 5 months ago by Bogdan170
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 4 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 4 months ago by Bogdan170
1
gravatar for Etal
4 months ago by
Etal1.4k
San Francisco, CA
Etal1.4k wrote:

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

ADD COMMENTlink written 4 months ago by Etal1.4k
1
gravatar for EagleEye
4 months ago by
EagleEye3.1k
Sweden
EagleEye3.1k wrote:

For array,

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

ADD COMMENTlink written 4 months ago by EagleEye3.1k
1
gravatar for chloe.steen
4 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 4 months ago by chloe.steen120
1
gravatar for Jeffin Rockey
4 months ago by
Jeffin Rockey240
Jeffin Rockey240 wrote:

Please see cn.MOPS also.

Jf

ADD COMMENTlink written 4 months ago by Jeffin Rockey240
1
gravatar for ssv.bio
4 months ago by
ssv.bio160
ssv.bio160 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 4 months ago • written 4 months ago by ssv.bio160
0
gravatar for Bogdan
4 months ago by
Bogdan170
United States
Bogdan170 wrote:

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

ADD COMMENTlink written 4 months ago by Bogdan170
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