Update Phylogeny of genotypes authored by Sophie Blanc's avatar Sophie Blanc
......@@ -7,6 +7,7 @@ Then variants were filtered again based on certain criteria. Were removed from f
- SOR (StrandOddsRatio) > 3.0
- MQ (RMSMappingQuality) < 40.0
For further information on criteria, take a look on the page below :
https://gatk.broadinstitute.org/hc/en-us/articles/360035890471-Hard-filtering-germline-short-variants
The phylogenic tree was generated using SNPhylo.20181005, with a bootstrap confidence value of 100, and using Pathenocissus as outgroup.