LOH segment inferring from WES data for germline sample

Question

[J.F.Jiang]

Hi all,

We applied WES to determine the pathogenic variants. Meanwhile, we want to check the LOH status of the sample.

We used CNVKit to calculate the CNV of the sample.

I am wondering is there a tool to get the LOH segment of the samples?

[German.M.Demidov]

Plink or roh hunter :) https://github.com/imgag/ngs-bits/blob/master/doc/tools/RohHunter.md