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im3sanger / dndscv

dN/dS methods to quantify selection in cancer and somatic evolution
GNU General Public License v3.0
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confidence intervals for gene-level dN/dS values and version for hg38 #13

Closed AlinaSc closed 6 years ago

AlinaSc commented 6 years ago

Hi,

I was just wondering if it is somehow possible to easily obtain gene level confidence intervals for the dN/dS values? And also, is there a version of the package for hg38? Hope you can help me!

Best, Alina

im3sanger commented 6 years ago

Hi Alina,

Thank you for your interest in dNdScv.

At present, only maximum likelihood estimates are provided for the dN/dS values at gene level. I will add your request to calculate confidence intervals to the list of future improvements.

At present, there is only support for hg37 but offering a general implementation of dndscv for any assembly or any species is a top priority for me. For now, you can use liftover to move your hg38 variants to hg37 to run dndscv.

Best wishes, Inigo