Can CVNkit call CNV correctly at HLA genes region?

Question

[MatthewP]

Hello, I use CNVkit to call CNV from WES data. I check my WES target region and find this include HLA genes region.

chr6    29691167        29691445        HLA-F
chr6    29691445        29691724        HLA-F
chr6    29691724        29692003        HLA-F
chr6    29692003        29692282        HLA-F
chr6    29692750        29693140        HLA-F
chr6    29693177        29693387        HLA-F
chr6    29693690        29693900        HLA-F
chr6    29694077        29694287        HLA-F
chr6    29694611        29695001        HLA-F,HLA-F-AS1
chr6    29695673        29695943        HLA-F-AS1
chr6    29704091        29704301        HLA-F-AS1
chr6    29759738        29760128        HCG4,HLA-V
chr6    29760153        29760543        HCG4,HLA-V
chr6    29764865        29765075        HLA-V
chr6    29794713        29794923        HLA-G
chr6    29795548        29795758        HLA-G

I want to know can CNVKIT call CNV good quality at those regions? I guess this depends on BWA alignment and Hybrid capture at HLA regions, so my answer is no. What do you think?

Answer 1

[linouhao]

facets maybe a good choice, but I do not know how to annotate the segement results

[MatthewP]

Thanks @linouhao. I don't need to handle those regions. All I want to discuss is what will affect CNVKIT performance at those regions.