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
+cd /exports/igmm/eddie/ISARIC4C/wp5-gwas/analysis/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
@@ -55,7 +55,7 @@ IlmnID,Name,IlmnStrand,SNP,AddressA_ID,AlleleA_ProbeSeq,AddressB_ID,AlleleB_Prob
 ### Compare by positions (**not alleles**)
 
 ```
-perl scripts/compare_UKB_GSA_array_tags.pl Axiom_UKB_WCSG.na34.annot.csv GSAMD-24v3-0-EA_20034606_A1.csv pos_only > compare_pos_only.txt 2> compare_pos_only.err
+perl ../../scripts/compare_UKB_GSA_array_tags.pl Axiom_UKB_WCSG.na34.annot.csv GSAMD-24v3-0-EA_20034606_A1.csv pos_only > compare_pos_only.txt 2> compare_pos_only.err
 cut -f 4 compare_pos_only.txt | sort | uniq -c
  279300 both
  435910 gsa_only
@@ -65,7 +65,7 @@ cut -f 4 compare_pos_only.txt | sort | uniq -c
 ### Compare by position and alleles
 
 ```
-perl scripts/compare_UKB_GSA_array_tags.pl Axiom_UKB_WCSG.na34.annot.csv GSAMD-24v3-0-EA_20034606_A1.csv alleles > compare_alleles.txt 2> compare_alleles.err
+perl ../../scripts/compare_UKB_GSA_array_tags.pl Axiom_UKB_WCSG.na34.annot.csv GSAMD-24v3-0-EA_20034606_A1.csv alleles > compare_alleles.txt 2> compare_alleles.err
 cut -f 6 compare_alleles.txt  | sort | uniq -c
  267308 both
  450562 gsa_only
@@ -92,7 +92,7 @@ wc -l rsids.*
   845485 rsids.ukb_all.txt
   576086 rsids.ukb_only.txt
 
-cat UKB_MAFs/* | perl scripts/extract_UKB_mafs_by_rsid.pl rsids.ukb_all.txt > mafs.ukb_all.txt
-cat UKB_MAFs/* | perl scripts/extract_UKB_mafs_by_rsid.pl rsids.ukb_only.txt > mafs.ukb_only.txt
-cat UKB_MAFs/* | perl scripts/extract_UKB_mafs_by_rsid.pl rsids.both.txt > mafs.both.txt
+cat UKB_MAFs/* | perl ../../scripts/extract_UKB_mafs_by_rsid.pl rsids.ukb_all.txt > mafs.ukb_all.txt
+cat UKB_MAFs/* | perl ../../scripts/extract_UKB_mafs_by_rsid.pl rsids.ukb_only.txt > mafs.ukb_only.txt
+cat UKB_MAFs/* | perl ../../scripts/extract_UKB_mafs_by_rsid.pl rsids.both.txt > mafs.both.txt
 ```
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