Intersection-between-UK-Biobank-and-Illumina-GSA-arrays.md

+## Fetch the UK Biobank MAFs
+
+```
+cd /exports/igmm/eddie/ISARIC4C/wp5-gwas/UKB_vs_GSA_tag_sites
+mkdir UKB_MAFs
+cd UKB_MAFs
+for i in 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 X XY
+do
+  wget http://biobank.ctsu.ox.ac.uk/crystal/crystal/auxdata/ukb_mfi_chr${i}_v3.txt
+done
+```
+
+## Get the array sites
+
+### UK Biobank
+
+```
+cd /exports/igmm/eddie/ISARIC4C/wp5-gwas/UKB_vs_GSA_tag_sites
+wget http://www.affymetrix.com/analysis/downloads/na34/genotyping/Axiom_UKB_WCSG.na34.annot.csv.zip
+unzip Axiom_UKB_WCSG.na34.annot.csv.zip
+rm Axiom_UKB_WCSG.na34.annot.csv.zip
+```
+
+### Illumina GSA
+
+```
+cp /exports/igmm/datastore/ISARIC4C/wp5-gwas/data/20200504/GSA-Multi\ Disease\ v3/GSAMD24v3-0_A1_gb37/GSAMD-24v3-0-EA_20034606_A1.csv  ./
+```
+
+## Counts and overlap
+
+Very rough count, including header lines:
+```
+wc -l *.csv
+    845507 Axiom_UKB_WCSG.na34.annot.csv
+    730091 GSAMD-24v3-0-EA_20034606_A1.csv
+```