update alspac ids

update_ids.sh

#!/bin/bash

cd /panfs/panasas01/shared/alspac/studies/latest/alspac/genetic/variants/arrays/gwas/imputed/1000genomes/released/27Feb2015/data/derived

mkdir -p ~/updated_ids
mkdir -p ~/updated_ids/kinships
mkdir -p ~/updated_ids/principal_components/all
mkdir -p ~/updated_ids/principal_components/unrelateds
mkdir -p ~/updated_ids/exclusion_ids
mkdir -p ~/updated_ids/unrelated_ids

cd kinships
awk '{ print $2, $2 }' hm3_autosomes.grm.id > ~/updated_ids/kinships/hm3_autosomes.grm.id

cd ../principal_components/all
awk '{ print $2, $2 }' children.eigenvec > ~/updated_ids/temp1
cut -d " " -f 3- children.eigenvec > ~/updated_ids/temp2
paste -d " " ~/updated_ids/temp1 ~/updated_ids/temp2 > ~/updated_ids/principal_components/all/children.eigenvec

awk '{ print $2, $2 }' mothers.eigenvec > ~/updated_ids/temp1
cut -d " " -f 3- mothers.eigenvec > ~/updated_ids/temp2
paste -d " " ~/updated_ids/temp1 ~/updated_ids/temp2 > ~/updated_ids/principal_components/all/mothers.eigenvec


cd ../unrelateds
awk '{ print $2, $2 }' children.eigenvec > ~/updated_ids/temp1
cut -d " " -f 3- children.eigenvec > ~/updated_ids/temp2
paste -d " " ~/updated_ids/temp1 ~/updated_ids/temp2 > ~/updated_ids/principal_components/unrelateds/children.eigenvec

awk '{ print $2, $2 }' mothers.eigenvec > ~/updated_ids/temp1
cut -d " " -f 3- mothers.eigenvec > ~/updated_ids/temp2
paste -d " " ~/updated_ids/temp1 ~/updated_ids/temp2 > ~/updated_ids/principal_components/unrelateds/mothers.eigenvec


cd ../unrelated_ids
awk '{ print $2, $2 }' children.txt > ~/updated_ids/unrelated_ids/children.txt
awk '{ print $2, $2 }' mothers.txt > ~/updated_ids/unrelated_ids/mothers.txt


cut -d "," -f 2-3 /panfs/panasas01/shared/alspac/ALSPAC_CONSENT_WITHDRAWN_LIST.csv | sed 1d | tr '-' 'M' | sed 's/,//g' > ~/updated_ids/exclusion_ids/exclusion_ids.txt

paste -d " " ~/updated_ids/exclusion_ids/exclusion_ids.txt ~/updated_ids/exclusion_ids/exclusion_ids.txt > ~/updated_ids/exclusion_ids/exclusion_ids.plink

awk '{ print $1, $2, "-9", "-9", "-9", "-9", "-9" }'  ~/updated_ids/exclusion_ids/exclusion_ids.plink > ~/updated_ids/temp2
echo -e "ID_1 ID_2 missing father mother sex plink_pheno\n0 0 0 D D D B" > ~/updated_ids/temp1
cat ~/updated_ids/temp1 ~/updated_ids/temp2 > ~/updated_ids/exclusion_ids/exclusion_ids.sample