It looks like you're new here. If you want to get involved, click one of these buttons!
I am calling SNPs and Indels on a non-mammalian genome and do not have an empirical truth set for either. What would you recommend are the annotations I can use for filtering out low-confidence calls?
Thanks for your input!
Then you're doing the right thing; carry on!
Geraldine Van der Auwera, PhD
I am following the hard filtering criteria listed here and it seems to be working well.