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CNV caller software

Dear all,

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

-- bogdan

cnv
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updated by Lemire Lemire • written by Bogdan Bogdan

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?

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written by Jared Evans Jared Evans

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 !

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written by Bogdan Bogdan

6 answers

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.

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written by cbst cbst

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

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written by Eric T. Eric T.

For array,

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

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written by EagleEye EagleEye

Please see cn.MOPS also.

Jf

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written by Jeffin Rockey Jeffin Rockey

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

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written by Bogdan Bogdan

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