Best CNV caller for Illumina WGRS data, in order to compare two phenotypes

Question

[hugocarmaga]

I'm new to CNV calling, and I would like to get advice on CNV callers to use. I have 30 Illumina WGRS paired-end 150bp libraries, belonging to two different phenotypes (14 for one and 16 for the other). I aim to study the possible influence of CNVs in the phenotype determination.

If someone with experience in CNV calling could give me a hint, it would be nice

[Medhat]

can you begin with reading Whole-genome CNV analysis: advances in computational approaches

[hugocarmaga]

Thanks. But at first sight I don't see some softwares I thought to be more used nowadays, like Canvas, Sequenza, FACETS or CNVkit. I just can't understand (probably because I'm new to bioinformatics also) which one suits better for my goals

[Medhat]

This was to give you a general idea about the CNV detection concepts.

Answer 1

[Eric T.]

If these sequenced samples are germline/non-lesional tissue, good-quality (fresh or frozen, not degraded), whole genomes at 30x coverage or higher, all sequenced according to the same protocol, and you're looking for relatively small-scale deletions specific to one phenotype or the other, then consider Canvas, cn.MOPS, or possibly the GATK4 CNV module. They are optimized for this type of study.

[hugocarmaga]

Thank you, I will follow your advice

[linouhao]

hi,do you kwow how to start canvas in Somatic-WGS, I do not know where is source UpdateEnvironmentMono and mono Canvas.exe Somatic-WGS,thanks a lot.