e82a8101c1aa495e0e6c841f83f4d6c980fddf49 max Thu Mar 12 07:28:49 2026 -0700 Add STRchive disease-associated STR loci track to strVar supertrack 75 curated disease-associated tandem repeat expansion loci from STRchive (Hiatt et al. 2025), with pathogenic thresholds, inheritance modes, and disease annotations. Colored by inheritance mode, refs #36652 Co-Authored-By: Claude Opus 4.6 diff --git src/hg/makeDb/doc/hg38/strchive.txt src/hg/makeDb/doc/hg38/strchive.txt new file mode 100644 index 00000000000..e84305e520d --- /dev/null +++ src/hg/makeDb/doc/hg38/strchive.txt @@ -0,0 +1,32 @@ +# STRchive disease-associated STR loci track (part of strVar supertrack) +# 2026-03-12 (max) + +# Data from STRchive (https://strchive.org/), CC BY 4.0 +# Paper: Hiatt et al. Genome Med 2025, PMID 40140942 +# 75 disease-associated tandem repeat expansion loci +# Curated from published literature by the Dashnow lab + +# Source: downloaded from GitHub +mkdir -p /hive/data/genomes/hg38/bed/str/strchive +cd /hive/data/genomes/hg38/bed/str/strchive +wget https://raw.githubusercontent.com/dashnowlab/STRchive/refs/heads/main/data/catalogs/STRchive-disease-loci.hg38.general.bed + +# Convert to BED9+ format (colored by inheritance mode) +python3 ~/kent/src/hg/makeDb/scripts/strchive/strchiveToBed.py \ + STRchive-disease-loci.hg38.general.bed > strchive.bed 2>/dev/null + +# Sort and convert to bigBed +bedSort strchive.bed strchive.bed +bedToBigBed strchive.bed /hive/data/genomes/hg38/chrom.sizes strchive.bb \ + -type=bed9+ -tab -as=$HOME/kent/src/hg/makeDb/scripts/strchive/strchive.as + +# Symlink into /gbdb (under webstr/ directory with other STR tracks) +ln -sf /hive/data/genomes/hg38/bed/str/strchive/strchive.bb /gbdb/hg38/webstr/strchive.bb + +# trackDb: strchive track is inside the strVar supertrack +# trackDb entry: ~/kent/src/hg/makeDb/trackDb/human/hg38/webstr.ra +# HTML doc: ~/kent/src/hg/makeDb/trackDb/human/hg38/strchive.html + +# Load trackDb +cd ~/kent/src/hg/makeDb/trackDb +make DBS=hg38