Lichee filters all variants as germline

Question

[Aidan.Matzko]

Hello,

I'm attempting to use Lichee to construct a phylogenetic tree. However, every one of my variants are being filtered as germline.

Sample input:

chrX    46887392        G/A_JADE3       0.0     0       0       0       0       0       0       0.403846153846

Error:

**Filtered as germline:
chr8    144945137       T/G_EPPK1       0.0     0       0       0       0       0       0.202857142857  0

How I'm running it:

./lichee -build -i output.trees -n 0 -maxVAFAbsent 1 -minVAFPresent 0 -dot

Thanks so much!

Answer 1

[Aidan.Matzko]

I figured it out on my own - the maxVAFAbsent and minVAFPresent flags need to be set to values such as .005 to work.