WES germline CNV caller for trio analysis

Question

[Nelson]

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!
Cheers!

Answer 1

[Eric T.]

Illumina's Canvas should work for your study.

[cc]

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.

Answer 2

[andrew.j.skelton73]

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.