2ec22bc5fa605aebe9576301f7f238566d61e9e8
max
  Tue Mar 10 04:00:22 2020 -0700
adding indexed files for aligners, refs #25100

diff --git src/hg/makeDb/doc/hg19.analysisSet.txt src/hg/makeDb/doc/hg19.analysisSet.txt
index aa327af..aae6fe8 100644
--- src/hg/makeDb/doc/hg19.analysisSet.txt
+++ src/hg/makeDb/doc/hg19.analysisSet.txt
@@ -22,20 +22,32 @@
 # not sure if anyone needs a 2bit file for these?
 faToTwoBit hg19.p13.plusMT.no_alt_analysis_set.fa.gz hg19.p13.plusMT.no_alt_analysis_set.2bit 
 faToTwoBit hg19.p13.plusMT.full_analysis_set.fa.gz hg19.p13.plusMT.full_analysis_set.2bit
 
 # make table for g1k genome
 twoBitInfo hg19.p13.plusMT.no_alt_analysis_set.2bit stdout | grep -v 'chrEBV' | grep -v 'chrM'$'\t' | sort -k2n > ucscSizes.noAlt.txt
 wget ftp://ftp-trace.ncbi.nih.gov/1000genomes/ftp/technical/reference/human_g1k_v37.fasta.gz 
 faSize -detailed human_g1k_v37.fasta.gz > g1k.sizes
 paste g1k.sizes ucscSizes.noAlt.txt |cut -f1,3 > g1kToUcsc.txt
 
 # make table for Ensembl genome
 wget http://ftp.ensembl.org/pub/grch37/release-99/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.dna_sm.primary_assembly.fa.gz 
 faSize -detailed Homo_sapiens.GRCh37.dna_sm.primary_assembly.fa.gz > ensemblSizes.txt &
 paste ensemblSizes.txt ucscSizes.noAlt.txt  | cut -f1,3 > ensemblToUcsc.txt
 
+# index for aligners
+mkdir hg19
+zcat hg19.p13.plusMT.no_alt_analysis_set.fa.gz > hg19/hg19.p13.plusMT.no_alt_analysis_set.fa
+cd hg19
+bwa index hg19.p13.plusMT.no_alt_analysis_set.fa
+bowtie2-build hg19.p13.plusMT.no_alt_analysis_set.fa hg19.p13.plusMT.no_alt_analysis_set
+hisat2-build hg19.p13.plusMT.no_alt_analysis_set.fa hg19.p13.plusMT.no_alt_analysis_set
+cd ..
+
+tar cvzf hg19.p13.plusMT.no_alt_analysis_set.bwa_index.tar.gz hg19/*.{pac,amb,ann,bwt,sa}
+tar cvzf hg19.p13.plusMT.no_alt_analysis_set.bowtie2_index.tar.gz hg19/*.bt2
+tar cvzf hg19.p13.plusMT.no_alt_analysis_set.hisat2_index.tar.gz hg19/*.ht2
+
 # copy stuff to webserver
 mkdir /usr/local/apache/htdocs-hgdownload/goldenPath/hg19/bigZips/analysisSet/chromAlias -p
-mv *.2bit /usr/local/apache/htdocs-hgdownload/goldenPath/hg19/bigZips/analysisSet/
-mv hg19.*.gz /usr/local/apache/htdocs-hgdownload/goldenPath/hg19/bigZips/analysisSet/
+mv *.2bit hg19.*.gz /usr/local/apache/htdocs-hgdownload/goldenPath/hg19/bigZips/analysisSet/
 mv *toUcsc.txt /usr/local/apache/htdocs-hgdownload/goldenPath/hg19/bigZips/analysisSet/chromAlias/