00e086afbcb8296c6aef946c13eeb777f34bac02
max
  Mon May 11 07:03:10 2026 -0700
mei: new track for HGSVC3 mobile element insertions on hg38 and hs1

12,642 MEIs on hg38, 12,919 on hs1, from the HGSVC3 callset (Logsdon
et al. 2025). Single shared trackDb stanza in human/mei.ra with $D
substitution. Okabe-Ito colors, INS-svLen:carrierCount item names,
inserted DNA in an insertSeq field. Cross-link to lrSv via
relatedTracks.ra. refs #37524

diff --git src/hg/makeDb/doc/hg38/mei.txt src/hg/makeDb/doc/hg38/mei.txt
new file mode 100644
index 00000000000..1ecd9be884c
--- /dev/null
+++ src/hg/makeDb/doc/hg38/mei.txt
@@ -0,0 +1,67 @@
+# 2026-05-09 Claude (max) - Mobile Element Insertions track collection (mei)
+# Source: HGSVC3 (Logsdon et al. 2025, Nature, PMID 40702183)
+# https://ftp.1000genomes.ebi.ac.uk/vol1/ftp/data_collections/HGSVC3/release/Mobile_Elements/1.0/
+# README: https://ftp.1000genomes.ebi.ac.uk/vol1/ftp/data_collections/HGSVC3/release/Mobile_Elements/1.0/README.20241211.MEI.txt
+
+# This track collection holds polymorphic Mobile Element Insertions (MEIs).
+# The first subtrack, meiHgsvc3, is the HGSVC3 MEI callset: mobile element
+# insertions identified in 65 long-read assembled samples relative to the
+# reference assembly. Two parallel callsets are released, one against
+# GRCh38 and one against T2T-CHM13, and we build a bigBed for each.
+# Each item is drawn as a 1-bp anchor block at the insertion attachment
+# site; per-sample genotypes are summarised into alt-allele count, allele
+# number, alt-allele frequency, and a list of carrier samples.
+
+############################################################
+# GRCh38 / hg38
+
+mkdir -p /hive/data/genomes/hg38/bed/mei
+cd /hive/data/genomes/hg38/bed/mei
+
+wget https://ftp.1000genomes.ebi.ac.uk/vol1/ftp/data_collections/HGSVC3/release/Mobile_Elements/1.0/MEI_Callset_GRCh38.ALL.20241211.csv.gz
+
+# Convert CSV (VCF-like, 65 sample genotype columns + Caller_Count,
+# TE_Designation, L1ME-AID, PALMER, L1ME-AID_INFO, PALMER_INFO,
+# PAVMergedCalls) to bed9+15. The script tallies per-record alt-allele
+# counts and carrier sample lists, and colors items by mobile element
+# class.
+# Source: ~/kent/src/hg/makeDb/scripts/mei/meiHgsvc3CsvToBed.py
+python3 ~/kent/src/hg/makeDb/scripts/mei/meiHgsvc3CsvToBed.py \
+    MEI_Callset_GRCh38.ALL.20241211.csv.gz \
+    /hive/data/genomes/hg38/chrom.sizes \
+    meiHgsvc3.bed
+# -> Read 12642 records, wrote 12642, skipped 0 + 0
+# Class distribution: Alu 10270, L1 1604, SVA 764, HERVK 3, snRNA 1.
+
+sort -k1,1 -k2,2n meiHgsvc3.bed > meiHgsvc3.sorted.bed
+
+bedToBigBed -tab \
+    -as=$HOME/kent/src/hg/makeDb/scripts/mei/meiHgsvc3.as \
+    -type=bed9+16 \
+    meiHgsvc3.sorted.bed \
+    /hive/data/genomes/hg38/chrom.sizes \
+    meiHgsvc3.bb
+
+############################################################
+# T2T-CHM13 / hs1
+
+mkdir -p /hive/data/genomes/hs1/bed/mei
+cd /hive/data/genomes/hs1/bed/mei
+
+wget https://ftp.1000genomes.ebi.ac.uk/vol1/ftp/data_collections/HGSVC3/release/Mobile_Elements/1.0/MEI_Callset_T2T-CHM13.ALL.20241211.csv.gz
+
+python3 ~/kent/src/hg/makeDb/scripts/mei/meiHgsvc3CsvToBed.py \
+    MEI_Callset_T2T-CHM13.ALL.20241211.csv.gz \
+    /hive/data/genomes/hs1/chrom.sizes \
+    meiHgsvc3.bed
+# -> Read 12919 records, wrote 12919, skipped 0 + 0
+# Class distribution: Alu 10458, L1 1664, SVA 791, HERVK 5, snRNA 1.
+
+sort -k1,1 -k2,2n meiHgsvc3.bed > meiHgsvc3.sorted.bed
+
+bedToBigBed -tab \
+    -as=$HOME/kent/src/hg/makeDb/scripts/mei/meiHgsvc3.as \
+    -type=bed9+16 \
+    meiHgsvc3.sorted.bed \
+    /hive/data/genomes/hs1/chrom.sizes \
+    meiHgsvc3.bb