e9cbd875e607d5774dfbc19ff8c389ff9ec851f6
braney
  Thu Feb 6 12:09:35 2025 -0800
make quickLift chain from hg19 to hg38

diff --git src/hg/makeDb/doc/hg19.txt src/hg/makeDb/doc/hg19.txt
index edae13789b6..5e04b713583 100644
--- src/hg/makeDb/doc/hg19.txt
+++ src/hg/makeDb/doc/hg19.txt
@@ -35648,15 +35648,35 @@
 ## $ 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
 #########################################################################
+
+# quickLift from hg19 to hg38
+mkdir -p /hive/data/genomes/hg19/bed/quickLiftChain
+cd  /hive/data/genomes/hg19/bed/quickLiftChain
+
+mkdir tmp
+cd tmp
+
+chainSwap ../../liftOver/hg19ToHg38.over.chain.gz hg19ToHg38.over.swap.chain
+
+awk '/chain/ {print $3, $4}' hg19ToHg38.over.swap.chain | sort | uniq > hg19ToHg38.over.swap.sizes
+chainToBigChain hg19ToHg38.over.swap.chain bigChainOut bigLinkOut
+bedToBigBed -type=bed6+6 -as=$HOME/kent/src/hg/lib/bigChain.as -tab bigChainOut hg19ToHg38.over.swap.sizes hg19ToHg38.bb
+bedToBigBed -type=bed4+1 -as=$HOME/kent/src/hg/lib/bigLink.as -tab bigLinkOut  hg19ToHg38.over.swap.sizes hg19ToHg38.link.bb
+
+ln -s `pwd`/hg19ToHg38.bb /gbdb/hg19/quickLift/hg38.bb
+ln -s `pwd`/hg19ToHg38.link.bb /gbdb/hg19/quickLift/hg38.link.bb
+hgsql hgcentraltest -Ne 'insert into quickLiftChain values (0, "hg19", "hg38", "/gbdb/hg19/quickLift/hg38.bb")'
+
+###