b96a4b4d3d3b9d7dd2e7a1934ff4e4e57fb1348b
angie
  Tue Feb 22 11:07:42 2022 -0800
Mask two new problematic-in-Delta positions (https://github.com/cov-lineages/pango-designation/issues/435)

diff --git src/hg/utils/otto/sarscov2phylo/maskDelta.sh src/hg/utils/otto/sarscov2phylo/maskDelta.sh
index 251119d..3bc7072 100755
--- src/hg/utils/otto/sarscov2phylo/maskDelta.sh
+++ src/hg/utils/otto/sarscov2phylo/maskDelta.sh
@@ -42,30 +42,35 @@
 done >> $maskFile
 echo -e "N28271N\t$deltaNode" >> $maskFile
 set -x
 
 # S:95 (21846) is also very unreliably detected in Delta.  Mask it off to avoid tree trouble,
 # like split AY.100.
 echo -e "N21846N\t$deltaNode" >> $maskFile
 
 # These three sites are recommended for caution in the Problematic Sites set, and seem to have
 # create a false lineage (AY.89) from samples that probably should be AY.4.  AY.89 is being
 # withdrawn (https://github.com/cov-lineages/pango-designation/issues/398); mask sites in Delta.
 echo -e "N21302N\t$deltaNode" >> $maskFile
 echo -e "N21304N\t$deltaNode" >> $maskFile
 echo -e "N21305N\t$deltaNode" >> $maskFile
 
+# Mask flaky positions 28254 (ORF8:121) and 28461 (N:63) so that AY.96 is merged into AY.46
+# https://github.com/cov-lineages/pango-designation/issues/435
+echo -e "N28254N\t$deltaNode" >> $maskFile
+echo -e "N28461N\t$deltaNode" >> $maskFile
+
 # OK, not just Delta -- Alpha, Beta, and Gamma have a deletion that causes spurious "mutations",
 # especially at 11296 and 11291, somewhat also at 11288.
 # Omicron has ~ the same deletion but it aligns 5 bases to the left, probably because it was
 # combined with an SNV (https://github.com/cov-lineages/pango-designation/issues/361).
 alphaNode=$(grep Italy/TAA-1900553896/2021 $samplePaths \
             | awk '{print $(NF-1);}' | sed -re 's/:.*//;')
 betaNode=$(grep SouthAfrica/CERI-KRISP-K012031/2021 $samplePaths \
            | awk '{print $NF;}' | sed -re 's/:.*//;')
 gammaNode=$(grep France/PAC-IHU-5193-N1/2021 $samplePaths | awk '{print $NF;}' | sed -re 's/:.*//;')
 set +x
 for node in $alphaNode $betaNode $gammaNode; do
     for ((i=11288;  $i <= 11296;  i++)); do
         echo -e "N${i}N\t$node"
     done
 done >> $maskFile