Post date: May 07, 2020 11:17:51 AM
After discussing with Will, I decided not to filter Pando against friends or PONs. What are the reasons to do the filtering?
- get rid of high mutation sites that are common to aspen in general
- get rid of systematic errors during the sequencing step
- get rid of somatic mutations that will be present in Pando and friends as they are close clones
To check with Zach + the relevance not to filter.
Go back to the vcf file before fitering, and extract the proba of being hets:
3527 pando_only_05.txt
7186 pando_only_20.txt
9745 pando_only_50.txt
11196 pando_only_80.txt