Update mask sites
@@ -59,12 +59,13 @@ partition_sequences:
mask:
# Number of bases to mask from the beginning and end of the alignment. These regions of the genome
# are difficult to sequence accurately.
- mask_from_beginning: 130
+ mask_from_beginning: 100
mask_from_end: 50
# Specific sites to mask in the reference genome's coordinates.
# These are 1-indexed coordinates of sites that have been identified as prone to sequencing errors.
- mask_sites: "18529 29849 29851 29853"
+ # Need to provide something here for the script to not crash, using "1" in this case
+ mask_sites: "1"
# TreeTime settings
refine:
