Question: WES germline CNV caller for trio analysis
gravatar for Nelson
20 months ago by
Nelson0 wrote:

Dear all,

I have a family trio of WES for analysis of an autosomal dominant condition. Variant calling of SNPs/indels does not detect any mutations in the relevant genes. My next step is to perform CNV analysis, however, most callers need reference sample WES BED/BAM for normalisation which I don't have. Is there any tool that can perform germline CNV analysis without reference sample normalisation?

Thanks a lot!

cnv wes • 1.3k views
ADD COMMENTlink modified 20 months ago by andrew.j.skelton735.8k • written 20 months ago by Nelson0
gravatar for Eric T.
20 months ago by
Eric T.2.5k
San Francisco, CA
Eric T.2.5k wrote:

Illumina's Canvas should work for your study.

ADD COMMENTlink modified 20 months ago • written 20 months ago by Eric T.2.5k

Hi, Eric

I have targeted sequencing data of 20 samples (NGS, orphan disease, not cancer). And the targeted capture region is about ~8M, located in a contiunous region on chr22. I just noticed that Canvas is suitable for Germline-WGS, Somatic-Enrichment,Somatic-WGS,Tumor-normal-enrichment,SmallPedigree-WGS.

I am wondering if Canvas is a appropriate for this kind of data? Or anyelse softs you may suggest?

Thanks a lot.

ADD REPLYlink written 19 months ago by cc10
gravatar for andrew.j.skelton73
20 months ago by
andrew.j.skelton735.8k wrote:

ExomeDepth would be able to use the other samples within the pedigree as a reference. Also, this blogpost is an excellent (albeit fairly old but not much has changed since it's writing), comparison of germline CNV calling from Eric Minikel at the Macarthur lab.

ADD COMMENTlink written 20 months ago by andrew.j.skelton735.8k
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