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/hg38/hg38.txt src/hg/makeDb/doc/hg38/hg38.txt
index 1f3dc1234db..fcbc04a4d06 100644
--- src/hg/makeDb/doc/hg38/hg38.txt
+++ src/hg/makeDb/doc/hg38/hg38.txt
@@ -7375,16 +7375,36 @@
 mv hg38.chromAlias.bb  hg38.chromAlias.noindexes.bb
 bigBedInfo -asOut hg38.chromAlias.noindexes.bb >hg38.chromAlias.as
 bigBedToBed hg38.chromAlias.noindexes.bb  hg38.chromAlias.bed
 bedToBigBed -tab -type=bed3+ -as=hg38.chromAlias.as hg38.chromAlias.bed -sizesIs2Bit  -extraIndex=ucsc,assembly,ensembl,genbank,refseq hg38.2bit hg38.chromAlias.bb
 
 ##############################################################################
 
 # ENCODE 4 TF rPeak Clusters - RM #34930 - Lou 12/19/24
 
 mkdir /hive/data/genomes/hg38/bed/ENCODEv4TFrPeaks
 cd /hive/data/genomes/hg38/bed/ENCODEv4TFrPeaks
 hubClone -download https://users.wenglab.org/gaomingshi/TF.rpeak.test.txt
 ln -s /hive/data/genomes/hg38/bed/ENCODEv4TFrPeaks/no_trim.TF_name.rPeaks.bb /gbdb/hg38/bbi/ENCODE4/TFrPeakClusters.bb
 ln -s /hive/data/genomes/hg38/bed/ENCODEv4TFrPeaks/no_trim.TF_name.decorator.bb /gbdb/hg38/bbi/ENCODE4/TFrPeakClustersDecorator.bb
 # Then just moved the files to the ENCODEv4TFrPeaks dir, moved/tweaked HTML and trackDb
+#########################################################################
+# 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/hg38/v101
+zcat /hive/data/outside/cosmic/ucsc_export.v101.hg38.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/hg38/chrom.sizes cosmic.bb -tab
+cd /gbdb/hg38/cosmic/
+ln -s /hive/data/outside/cosmic/hg38/v98/cosmic.bb cosmicv98.bb
+ln -sf /hive/data/outside/cosmic/hg38/v101/cosmic.bb
+#Updated human/hg38/trackDb.ra and human/hg38/cosmicMuts.html
+#########################################################################