4d29f5bdc54732fe9518cf0357fb563074a1a238
kate
  Thu Sep 10 15:10:29 2020 -0700
More make doc. refs #26129

diff --git src/hg/makeDb/doc/covid/covidHgiGwas.txt src/hg/makeDb/doc/covid/covidHgiGwas.txt
index 259060a..373a78d 100644
--- src/hg/makeDb/doc/covid/covidHgiGwas.txt
+++ src/hg/makeDb/doc/covid/covidHgiGwas.txt
@@ -1,25 +1,25 @@
 # GWAS from the COVID-19 Host Genetics Initiative (HGI)
 # (2020-07-02 kate)
 
 # From: covid19hg.org/results
 
 # Contacts:  Rachel Liao,  Juha Karjalainen (Broad)
 juha.karjalainen@helsinki.fi
 
 # Create build dir
-cd /hive/data/outside/covidHostGenetics
+cd /hive/data/outside/covid/covidHostGenetics
 
 # GWAS meta-analyses file format
 
 1 #CHR    chromosome
 2 POS     chromosome position in build 37
 3 REF     non-effect allele
 4 ALT     effect allele (beta is for this allele)
 5 SNP     #CHR:POS:REF:ALT
 {STUDY}_AF_Allele2      allele frequency in {STUDY}
 {STUDY}_AF_fc   allele frequency in {STUDY} / allele frequency in gnomAD v3 (1000000 if frequency in gnomAD is 0). Calculated based on each study's ancestry in gnomAD
 {STUDY}_N
 6 + (X = #studies * 3) all_meta_N      number of studies that had the variant after AF and INFO filtering and as such were used for the meta
 7 + X all_inv_var_meta_beta   effect size on log(OR) scale
 8 + X all_inv_var_meta_sebeta standard error of effect size
 9 + X all_inv_var_meta_p      p-value