ee98569fb749e16cf3e4601a7cef331432d062f8
jeltje.van.baren
  Tue Jan 21 10:25:19 2025 -0800
adding alphaMissense

diff --git src/hg/makeDb/doc/hg19.txt src/hg/makeDb/doc/hg19.txt
index edb3197e5e1..20f17740861 100644
--- src/hg/makeDb/doc/hg19.txt
+++ src/hg/makeDb/doc/hg19.txt
@@ -35608,15 +35608,32 @@
 # Adjust the BED file for bigBed conversion:
 # prepends 'chr' to chromosome numbers, subtracts 1 from the start position, and adjusts fields for bigBed
 awk 'BEGIN{OFS="\t"} {print "chr"$1, $2-1, $3, $4, 0, ".", $2, $3, 0, $5, $6, $7, $8, $9, $10, $11, $12, $13, $14, $15}' population_cnv_grch37_final.bed > population_cnv_grch37_final_chr.bed
 
 bedSort population_cnv_grch37_final_chr.bed population_cnv_grch37_sorted.bed
 
 # Add RGB colors to the BED file using a Python script:
 python3  assign_rgb_to_bed.py population_cnv_grch37_sorted.bed output_population_cnv_grch37.bed
 
 bedToBigBed -type=bed9+ -as=bedExample2.as -tab -extraIndex=name output_population_cnv_grch37.bed hg19.chrom.sizes population_cnv_grch37.bb
 
 # Moving files
 cp /hive/users/gperez2/tracks/decipher/hg19/population_cnv_grch37.bb /hive/data/genomes/hg19/bed/decipher/population_cnv.bb
 
 ln -s /hive/data/genomes/hg19/bed/decipher/population_cnv.bb /gbdb/hg19/decipher/population_cnv.bb
+
+##############################################################################
+# alphaMissense ticket #32269 (Jeltje, Jan 2025)
+# based on REVEL and CADD
+mkdir -p /hive/data/genomes/hg19/bed/alphaMissense/
+cd /hive/data/genomes/hg19/bed/alphaMissense
+wget https://storage.googleapis.com/dm_alphamissense/AlphaMissense_hg19.tsv.gz
+time python ~/kent/src/hg/makeDb/outside/alphaMissense/alphaMissenseToWig.py AlphaMissense_hg19.tsv.gz
+wigToBigWig a.wig ../../chrom.sizes a.bw &
+wigToBigWig c.wig ../../chrom.sizes c.bw &
+wigToBigWig g.wig ../../chrom.sizes g.bw &
+wigToBigWig t.wig ../../chrom.sizes t.bw &
+wait
+
+# #Colors were added using the script
+kent/src/hg/makeDb/scripts/wigColorByColors/makeWigColorByRevelCadd.py
+