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Updated paths to match directory structure authored by ameyner2's avatar ameyner2
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Intersection-between-UK-Biobank-and-Illumina-GSA-arrays.md
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## Fetch the UK Biobank MAFs ## 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 mkdir UKB_MAFs
cd 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 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 ...@@ -55,7 +55,7 @@ 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 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 cut -f 4 compare_pos_only.txt | sort | uniq -c
279300 both 279300 both
435910 gsa_only 435910 gsa_only
...@@ -65,7 +65,7 @@ cut -f 4 compare_pos_only.txt | sort | uniq -c ...@@ -65,7 +65,7 @@ cut -f 4 compare_pos_only.txt | sort | uniq -c
### Compare by position and alleles ### 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 cut -f 6 compare_alleles.txt | sort | uniq -c
267308 both 267308 both
450562 gsa_only 450562 gsa_only
...@@ -92,7 +92,7 @@ wc -l rsids.* ...@@ -92,7 +92,7 @@ wc -l rsids.*
845485 rsids.ukb_all.txt 845485 rsids.ukb_all.txt
576086 rsids.ukb_only.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_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.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.both.txt > mafs.both.txt
``` ```
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