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

@@ -55,9 +55,26 @@ 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 > compare.txt 2> compare.err
-cut -f 4 compare.txt | sort | uniq -c
+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
  542810 ukb_only
 ```
+
+### 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
+cut -f 6 compare_alleles.txt  | sort | uniq -c
+ 267308 both
+ 450562 gsa_only
+ 558618 ukb_only
+```
+
+| Array | Match status | Position only | Allele + position match |
+|---|---|---|---|
+| UKB | Unique | 542810 / 66.0% | 558618 / 67.6% |
+| UKB | Both | 279300 / 34.0% | 267308 / 32.4% |
+| GSA | Unique | 435910 / 60.9% | 450562 / 62.8% |
+| GSA | Both | 279300 / 39.1% | 267308 / 37.2% |