Changes

Page history
Compare by positions only or alleles + positions authored by ameyner2's avatar ameyner2
Show whitespace changes
Inline Side-by-side
Intersection-between-UK-Biobank-and-Illumina-GSA-arrays.md
View page @ aa0c9984
...@@ -55,9 +55,26 @@ IlmnID,Name,IlmnStrand,SNP,AddressA_ID,AlleleA_ProbeSeq,AddressB_ID,AlleleB_Prob ...@@ -55,9 +55,26 @@ IlmnID,Name,IlmnStrand,SNP,AddressA_ID,AlleleA_ProbeSeq,AddressB_ID,AlleleB_Prob
### Compare by positions (**not alleles**) ### 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 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.txt | sort | uniq -c cut -f 4 compare_pos_only.txt | sort | uniq -c
279300 both 279300 both
435910 gsa_only 435910 gsa_only
542810 ukb_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% |