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dariober / cnv_facets

Somatic copy variant caller (CNV) for next generation sequencing
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difference between LOH and DUP-LOH #53

Closed guillaume-rs closed 1 year ago

guillaume-rs commented 1 year ago

Hello, I've used CNV_facets to detect LOH on multiple samples. I'm wondering what in the difference between LOH and DUP-LOH SV type present in the vcf output? Thanks, Guillaume

dariober commented 1 year ago

Hi Guillaume - See if this discussion helps https://github.com/mskcc/facets/issues/62 and in particular see the table I post there.

I'm closing the issue now but feel free to re-open it.

guillaume-rs commented 1 year ago

Hi Dario, Thank you for this link I understand better now. Just to be sure : If SVTYPE= LOH it has to be a copy neutral LOH? (tcn.em = 2 and lcn.em = 0) For LOH brought by the deletion of one chromosome they are annotated as HEMIZYGOTE? are all HEMIZYGOTE SVTYPE LOH event?