46f3b4d35904ddc3df91e916ad15c05ad878b3d1
lrnassar
  Thu May 21 08:02:58 2026 -0700
Adding PMS2 Pseudogene Caution track to InSiGHT hub. refs #36582

diff --git src/hg/makeDb/doc/InSiGHT.txt src/hg/makeDb/doc/InSiGHT.txt
index 1f49a3e32fd..59a95fca4d9 100644
--- src/hg/makeDb/doc/InSiGHT.txt
+++ src/hg/makeDb/doc/InSiGHT.txt
@@ -15,30 +15,31 @@
 
 # Quick link for github:
 # https://github.com/ucscGenomeBrowser/kent/tree/master/src/hg/makeDb/scripts/insight
 
 # Hub structure:
 #   /hive/users/lrnassar/insightHub/
 #     hub.txt, genomes.txt
 #     hg38/trackDb.txt, hg19/trackDb.txt
 #     insight.html (shared description page)
 #     clinDomains/   - Clinical Domains track data
 #     pvs1/          - PVS1 Regions track data
 #     afFrequencies/ - Allele Frequencies track data
 #     hciPriors/     - HCI Priors track data
 #     functionalAssays/ - Functional Assays track data
 #     lovdVars/      - InSiGHT Curated Variants track data
+#     pms2Caution/   - PMS2 Pseudogene Caution track data
 
 # Canonical transcripts used across all tracks:
 #   MLH1: NM_000249.4 (chr3, + strand)
 #   MSH2: NM_000251.3 (chr2, + strand)
 #   MSH6: NM_000179.3 (chr2, + strand)
 #   PMS2: NM_000535.7 (chr7, - strand)
 
 ##############################################################################
 # Track 1: Clinical Domains (PM1)
 ##############################################################################
 
 # Clinically relevant protein domains for the 4 MMR genes.
 # Domain definitions are hardcoded in the script from the InSiGHT VCEP specs.
 # Generates bigBed 9+4 files for hg38 and hg19.
 
@@ -124,33 +125,52 @@
 ##############################################################################
 # Track 6: InSiGHT Curated Variants (from ClinVar)
 ##############################################################################
 
 # InSiGHT VCEP expert panel classifications fetched from ClinVar API.
 # Queries ClinVar for variants submitted by InSiGHT on MLH1, MSH2, MSH6, PMS2.
 # No local data files needed -- fetches directly from NCBI E-utilities.
 # This is the track that should be periodically rebuilt (ClinVar updates monthly).
 # Generates bigBed 9+7 files for hg38 and hg19.
 
 cd /hive/users/lrnassar/insightHub/lovdVars
 python3 ~/kent/src/hg/makeDb/scripts/insight/buildInsightClinVar.py
 
 # Output: insightClinVarHg38.bb, insightClinVarHg19.bb
 
+##############################################################################
+# Track 7: PMS2 Pseudogene Caution Regions
+##############################################################################
+
+# PMS2 exons with high sequence homology to the PMS2CL pseudogene, plus the
+# PMS2CL pseudogene region itself. Flags regions where short-read NGS variant
+# calls may be pseudogene-derived. Per-exon caution levels:
+#   Exons 1-8, 10:  Safe (no homology)
+#   Exon 9:         Moderate (~98% homology)
+#   Exons 11-15:    High (>=99% homology)
+#   PMS2CL:         Pseudogene region (chr7:6,735,304-6,751,601 hg38)
+# Generates bigBed 9+5 files for hg38 and hg19.
+
+cd /hive/users/lrnassar/insightHub/pms2Caution
+python3 ~/kent/src/hg/makeDb/scripts/insight/insightPMS2Caution.py
+
+# Output: InSiGHTPMS2CautionHg38.bb, InSiGHTPMS2CautionHg19.bb
+
 ##############################################################################
 # Hub deployment
 ##############################################################################
 
 # The hub is served from:
 #   https://hgwdev-lrnassar.gi.ucsc.edu/~lrnassar/track_hubs/insightHub/hub.txt
 #
 # The public_html symlink points to the working directory:
 #   /cluster/home/lrnassar/public_html/track_hubs/insightHub -> /hive/users/lrnassar/insightHub
 #
 # To rebuild all tracks from scratch:
 cd /hive/users/lrnassar/insightHub
 cd clinDomains && python3 ~/kent/src/hg/makeDb/scripts/insight/insightClinDomains.py && cd ..
 cd pvs1 && python3 ~/kent/src/hg/makeDb/scripts/insight/insightPVS1.py && cd ..
 cd afFrequencies && python3 ~/kent/src/hg/makeDb/scripts/insight/insightAFfrequencies.py && cd ..
 cd hciPriors && python3 ~/kent/src/hg/makeDb/scripts/insight/insightHCIPriors.py && cd ..
 cd functionalAssays && python3 ~/kent/src/hg/makeDb/scripts/insight/insightFunctionalAssays.py && cd ..
 cd lovdVars && python3 ~/kent/src/hg/makeDb/scripts/insight/buildInsightClinVar.py && cd ..
+cd pms2Caution && python3 ~/kent/src/hg/makeDb/scripts/insight/insightPMS2Caution.py && cd ..