b62b289568697d98f019a4bd82bb910b044cbeb7 kate Tue Sep 15 15:27:20 2020 -0700 Support for use of lolly size, and pvalue displayed as E notation. refs #26129 diff --git src/hg/makeDb/doc/covid/covidHgiGwas.txt src/hg/makeDb/doc/covid/covidHgiGwas.txt index 373a78d..c9ee1c0 100644 --- src/hg/makeDb/doc/covid/covidHgiGwas.txt +++ src/hg/makeDb/doc/covid/covidHgiGwas.txt @@ -1,127 +1,134 @@ # 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/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 10 + X all_inv_var_het_p p-value from Cochran's Q heterogeneity test # additional columns: 11 + X "all_meta_sample_N" 12 + X "all_meta_AF" 13 + X "rsid" # additional for hg19 liftover. Values in hg38. 14 + X "anew_chr" 15 + X "anew_pos" 16 + X "REF.1" 17 + X "ALT.1" # Studies 1 Genetic determinants of COVID-19 complications in the Brazilian population BRACOVID 2 Genetic modifiers for COVID-19 related illness BelCovid 3 deCODE DECODE 4 FinnGen FinnGen 5 GEN-COVID, reCOVID GENCOVID 6 UK 100,000 Genomes Project genomicsengland100kgp_EUR 7 Genes & Health GNH 8 Generation Scotland GS 9 COVID19-Host(a)ge HOSTAGE 10 Helix Exome+ COVID-19 Phenotypes Helix 11 UK Blood Donors Cohort INTERVAL 12 LifeLines CytoSNP LifelinesCyto 13 LifeLines Global Screening Array LifelinesGsa 14 Netherlands Twin Register NTR 15 Partners Healthcare Biobank PHBB 16 Qatar Genome Program QGP 17 UK Biobank UKBB ##################### # Consult with Ana on Aug 12 1. Restrict to analyses with enough power (based on plots): B2: hospitalized covid vs. population (3199 cases, 8 studies) C2: covid vs. population (6696 cases, 18 studies) 2. Label options: rsID and/or ALT/REF (use ALT/REF if no label) 3. Mouseover: pValue, effect size, #studies 4. Filters: pValue (default=5), #studies, ###################### # Make with new .as (input from Juha), and hg38 tracks # (2020-09-04 kate) # Analysis B2: hospitalized covid vs. population # cases: 3199 # studies: 8 # Analysis C2: covid vs. population # cases: 6696 # studies: 18 # download hg19 files wget https://storage.googleapis.com/covid19-hg-public/20200619/results/build_37/COVID19_HGI_ANA_B2_V2_20200701.b37.txt.gz wget https://storage.googleapis.com/covid19-hg-public/20200619/results/build_37/COVID19_HGI_ANA_C2_V2_20200701.b37.txt.gz # download hg38 files wget https://storage.googleapis.com/covid19-hg-public/20200619/results/COVID19_HGI_ANA_B2_V2_20200701.txt.gz wget https://storage.googleapis.com/covid19-hg-public/20200619/results/COVID19_HGI_ANA_C2_V2_20200701.txt.gz gunzip *.z wc -l covidHgiGwas*.hg38.txt 15392647 covidHgiGwas.B2.hg38.txt 24600933 covidHgiGwas.C2.hg38.txt # rename ln -s COVID19_HGI_ANA_B2_V2_20200701.txt covidHgiGwas.B2.hg38.txt ln -s COVID19_HGI_ANA_C2_V2_20200701.txt covidHgiGwas.C2.hg38.txt ln -s COVID19_HGI_ANA_B2_V2_20200701.b37.txt covidHgiGwas.B2.hg19.txt ln -s COVID19_HGI_ANA_C2_V2_20200701.b37.txt covidHgiGwas.C2.hg19.txt wc -l covidHgiGwas* 15392647 covidHgiGwas.B2.hg38.txt 24600933 covidHgiGwas.C2.hg38.txt mkdir -p /gbdb/hg19/covidHgiGwas /gbdb/hg38/covidHgiGwas cat > makeHgi.csh << 'EOF' -set bin = ~/kent/src/makeDb/outside/covid +set bin = ~/kent/src/hg/makeDb/outside/covid foreach d (B2.hg19 B2.hg38 C2.hg19 C2.hg38) set db = $d:e set a = $d:r set sizes = /hive/data/genomes/$db/chrom.sizes - set f = covidHgiGwas$a.$db - echo $f.txt - perl $bin/makeCovidHgiGwas.pl $db $f.txt > $f.bed + set b = covidHgiGwas + set f = $b.$a.$db + set bb = $b$a.$db + echo $b.$a.$db + if ($a == "B2") then + set studies = 8 + else + set studies = 18 + endif + perl $bin/makeCovidHgiGwas.pl $db $studies $f.txt > $f.bed bedSort $f.bed $f.sorted.bed - bedToBigBed -type=bed9+10 -as=$bin/covidHgiGwas.as -tab $f.sorted.bed $sizes $f.bb - ln -s `pwd`/$f.bb /gbdb/hg19/covidHgiGwas + bedToBigBed -type=bed9+12 -as=$bin/covidHgiGwas.as -tab $f.sorted.bed $sizes $bb.bb + ln -s `pwd`/$bb.bb /gbdb/hg19/covidHgiGwas end 'EOF' make makeHgi.csh >&! makeHgi.out &