a8284e2d5f9f74b52d107a8b99de3e8a03a263a2
lrnassar
  Tue May 26 11:09:11 2026 -0700
Adding PMS2CL Paralog Variants track to InSiGHT hub. Projects PMS2 curated ClinVar variants onto PMS2CL coordinates to help analysts recognize PMS2CL calls that may correspond to known PMS2 variants. refs #36582

diff --git src/hg/makeDb/doc/InSiGHT.txt src/hg/makeDb/doc/InSiGHT.txt
index 59a95fca4d9..b3dc98eaaa1 100644
--- src/hg/makeDb/doc/InSiGHT.txt
+++ src/hg/makeDb/doc/InSiGHT.txt
@@ -123,50 +123,70 @@
 # Output: insightFunctionalAssaysHg38.bb, insightFunctionalAssaysHg19.bb
 
 ##############################################################################
 # 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
+# Output:
+#   insightClinVarHg38.bb, insightClinVarHg19.bb (curated variants track)
+#   pms2clParalogVarsHg38.bb, pms2clParalogVarsHg19.bb (PMS2CL paralog
+#     projection track -- built in the same script run, see Track 8 below)
 
 ##############################################################################
 # 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
 
+##############################################################################
+# Track 8: PMS2CL Paralog Variants
+##############################################################################
+
+# PMS2 curated variants from Track 6 projected onto PMS2CL coordinates, to help
+# analysts recognize when a PMS2CL call may correspond to a known PMS2 variant.
+# Uses the cDNA alignment between NM_000535.7 and NR_002217.1 with offset:
+#   PMS2 c. = PMS2CL n. + 1060 (most of the homologous region)
+#   PMS2 c. = PMS2CL n. + 903  (exon 9)
+#   PMS2 c. = PMS2CL n. + 1059 (exon 11 before the 1-bp indel)
+# Built as part of the buildInsightClinVar.py run (Track 6).
+# Generates bigBed 9+5 files for hg38 and hg19. ~36 projected variants.
+
+# (No separate command -- comes out of the Track 6 build above.)
+
+# Output: pms2clParalogVarsHg38.bb, pms2clParalogVarsHg19.bb (in lovdVars/)
+
 ##############################################################################
 # 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 ..