557e23cb23716c1e543903446c03bb3ed7a5a195
mspeir
  Fri Oct 15 15:31:42 2021 -0700
adding details about other files used, refs #27947

diff --git src/hg/makeDb/doc/hg38/gtex.txt src/hg/makeDb/doc/hg38/gtex.txt
index a9094e0..504f861 100644
--- src/hg/makeDb/doc/hg38/gtex.txt
+++ src/hg/makeDb/doc/hg38/gtex.txt
@@ -139,31 +139,34 @@
 
 ### TODO 
 # Add GTEx to Gene Sorter (2016-08-18 kate)
 # See hg/near/makeNear.doc
 
 #############################################################################
 # GTEx V8 cis-eQTLs CAVIAR High Confidence (Sept 2021) Matt
 
 cd /hive/data/genomes/hg38/bed/gtex/V8/eQtl/finemap_CAVIAR
 
 # Tar files were downloaded from https://gtexportal.org/home/datasets#filesetFilesDiv15
 # This file was used for this track:
 wget https://storage.googleapis.com/gtex_analysis_v8/single_tissue_qtl_data/GTEx_v8_finemapping_CAVIAR.tar
 # Then unpacked
 # Other files used:
-
+# Lookup table for all variants genotyped in GTEx
+wget https://storage.googleapis.com/gtex_analysis_v8/reference/GTEx_Analysis_2017-06-05_v8_WholeGenomeSeq_838Indiv_Analysis_Freeze.lookup_table.txt.gz
+# Gene-level model based on the GENCODE 26 transcript model, where isoforms were collapsed to a single transcript per gene.
+wget https://storage.googleapis.com/gtex_analysis_v8/reference/gencode.v26.GRCh38.genes.gtf
 
 # Initially planned to use this file: # CAVIAR_Results_v8_GTEx_LD_HighConfidentVariants.gz
 # as it seemed to be a filtered subset of eQTLs
 # Description from GTEx_v8_finemapping_CAVIAR/README.txt
 # ***CAVIAR_Results_v8_GTEx_LD_HighConfidentVariants.gz --> is a single file for all GTEx tissues and all eGene where we report
 # all the high causal variants (variants that have posterior probability of > 0.1).
 
 # Sample header line:
 # TISSUE  GENE    eQTL    CHROM   POS     Probability
 # Brain_Caudate_basal_ganglia     ENSG00000248485.1       1_161274374     1       161274374       0.157456
 
 # However, the names/positions in the eQTL column are not unique meaning
 # We want file with unique variant/eQTL names that match those in the GTEx
 # variant mapping file: GTEx_Analysis_2017-06-05_v8_WholeGenomeSeq_838Indiv_Analysis_Freeze.lookup_table.txt.gz
 # Looks like the CAVIAR_Results_v8_GTEx_LD_ALL_NOCUTOFF_with_Allele.txt.gz has names