f422617243b87c9c932331c7bbaba93c5a8381a6
gperez2
  Fri Jan 24 16:40:27 2025 -0800
Adding the v101 COSMIC track for hg38/hg19, refs #34904

diff --git src/hg/makeDb/doc/hg19.txt src/hg/makeDb/doc/hg19.txt
index e779add90c4..edae13789b6 100644
--- src/hg/makeDb/doc/hg19.txt
+++ src/hg/makeDb/doc/hg19.txt
@@ -35628,15 +35628,35 @@
 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
 
 ##############################################################################
 # VarChat ticket #35081 (Lou, Jan 2025)
 # See makedoc in makeDb/doc/hg38/varChat.txt
+#########################################################################
+# COSMIC v101 (01-24-2025) Gerardo
+# RM 34904
+
+# Karen from COSMIC emailed data files links to Max. Max renamed the files to make it clear which db they belong to.
+## $ ll /hive/data/outside/cosmic/ucsc_export*.bed.gz
+## rw-rw-r- 1 max protein 198M Jan 14 16:15
+## /hive/data/outside/cosmic/ucsc_export.v101.hg19.bed.gz
+## rw-rw-r- 1 max protein 198M Jan 14 13:35
+## /hive/data/outside/cosmic/ucsc_export.v101.hg38.bed.gz
+
+mkdir -p /hive/data/outside/cosmic/{hg19,hg38}/v101
+
+cd /hive/data/outside/cosmic/hg19/v101
+zcat /hive/data/outside/cosmic/ucsc_export.v101.hg19.bed.gz  | awk -F'\t' -v OFS="\t" '{ print $1, $2, $3, $7, 0, $6, $4, $5, $8 }' | sort -k1,1 -k2,2n > cosmic.bed
+bedToBigBed -type=bed6+3 -as=/hive/data/outside/cosmic/hg38/v98/cosmic.as cosmic.bed /hive/data/genomes/hg19/chrom.sizes cosmic.bb -tab
+cd /gbdb/hg19/cosmic/  
+ln -s /hive/data/outside/cosmic/hg19/v101/cosmic.bb 
+#Updated human/hg19/trackDb.ra and copied human/hg38/cosmicMuts.html to human/hg19
+#########################################################################