6ab7b1dfca6cc123dfe09a9e9f8afdf0c8cbdf31 max Mon Apr 20 06:40:58 2026 -0700 changes after code review, refs #37376 diff --git src/hg/makeDb/doc/hg38/strVar.txt src/hg/makeDb/doc/hg38/strVar.txt index 7c313ad7279..d8d58ccdcd1 100644 --- src/hg/makeDb/doc/hg38/strVar.txt +++ src/hg/makeDb/doc/hg38/strVar.txt @@ -32,30 +32,31 @@ # All four subtracks (webstr, tommoStr, trexplorer, viennaVntr) were recolored # from motif-period-based coloring to expected heterozygosity: # het = 1 - sum(p_i^2), blue (low) -> red (high) # # Color bins: # het < 0.1: dark blue (0,0,180) # 0.1-0.3: medium blue (70,130,230) # 0.3-0.5: light purple (180,130,200) # 0.5-0.7: salmon (230,100,80) # >= 0.7: dark red (180,0,0) # no data: gray (128,128,128) # webstr: het pooled across 5 1000G populations weighted by sample count cd /hive/data/genomes/hg38/bed/str/webstr +# Received the dump file from Melissa Gymrek by email. Alas, webstr has no good download file yet. python3 ~/kent/src/hg/makeDb/scripts/webstr/webstrToBed.py WebSTRDataDumpForMax \ > webstr.bed sort -k1,1 -k2,2n webstr.bed > webstr.sorted.bed bedToBigBed -type=bed9+ -tab \ -as=$HOME/kent/src/hg/makeDb/scripts/webstr/webstr.as \ webstr.sorted.bed /hive/data/genomes/hg38/chrom.sizes webstr.bb rm webstr.bed webstr.sorted.bed # tommoStr: het from allele count histogram (single Japanese population) cd /hive/data/genomes/hg38/bed/str/tommo python3 ~/kent/src/hg/makeDb/scripts/tommoStr/tommoStrToBed.py \ expansion-hunter-61KJPN-panel-export.reheader.vcf.gz > tommoStr.bed sort -k1,1 -k2,2n tommoStr.bed > tommoStr.sorted.bed bedToBigBed -type=bed9+ -tab \ -as=$HOME/kent/src/hg/makeDb/scripts/tommoStr/tommoStr.as \