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01a_extract_data_fields.sh
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01a_extract_data_fields.sh
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#!/bin/bash
#SBATCH -J extract_data_fields
#SBATCH -o extract_data_fields.o%j
#SBATCH -e extract_data_fields.o%j
#SBATCH -p normal
#SBATCH -N 1
#SBATCH -n 1
#SBATCH -t 10:00:00
#SBATCH -A OTH21148
#SBATCH [email protected]
#SBATCH --mail-type=begin
#SBATCH --mail-type=end
file_handlers='/work/06568/joyce_w/stampede2/software/ukbconv'
# Sex chromosome aneuploidy
$file_handlers/ukbconv \
$file_handlers/ukb45020.enc_ukb \
txt \
-s22019 \
-odata/extracted_data_fields/sex_chrom_aneuploidy
# Self-reported sex
$file_handlers/ukbconv \
$file_handlers/ukb45020.enc_ukb \
txt \
-s31 \
-odata/extracted_data_fields/reported_sex
# Sex determined from genotyping analysis
$file_handlers/ukbconv \
$file_handlers/ukb45020.enc_ukb \
txt \
-s22001 \
-odata/extracted_data_fields/genetic_sex
# Outliers for heterozygosity or missing rate
$file_handlers/ukbconv \
$file_handlers/ukb45020.enc_ukb \
txt \
-s22027 \
-odata/extracted_data_fields/outlier_heterozygosity
# Genotype missingness
$file_handlers/ukbconv \
$file_handlers/ukb45020.enc_ukb \
txt \
-s22005 \
-odata/extracted_data_fields/genotype_missingness
# Genetic kinship
$file_handlers/ukbconv \
$file_handlers/ukb45020.enc_ukb \
txt \
-s22021 \
-odata/extracted_data_fields/genetic_kinship
# Age
$file_handlers/ukbconv \
$file_handlers/ukb45020.enc_ukb \
txt \
-s21022 \
-odata/extracted_data_fields/age
# PC
$file_handlers/ukbconv \
$file_handlers/ukb45020.enc_ukb \
txt \
-s22009 \
-odata/extracted_data_fields/pc
# Ethnic background
$file_handlers/ukbconv \
$file_handlers/ukb45020.enc_ukb \
txt \
-s21000 \
-odata/extracted_data_fields/ethnic_background
# Caucasian as determined by genetics
$file_handlers/ukbconv \
$file_handlers/ukb45020.enc_ukb \
txt \
-s22006 \
-odata/extracted_data_fields/caucasian
# Genotype array used
$file_handlers/ukbconv \
$file_handlers/ukb45020.enc_ukb \
txt \
-s22006 \
-odata/extracted_data_fields/array_type
# Townsend deprivation index
$file_handlers/ukbconv \
$file_handlers/ukb45020.enc_ukb \
txt \
-s189 \
-odata/extracted_data_fields/townsend
# Total household income
$file_handlers/ukbconv \
$file_handlers/ukb45020.enc_ukb \
txt \
-s738 \
-odata/extracted_data_fields/income
# Educational attainment
$file_handlers/ukbconv \
$file_handlers/ukb45020.enc_ukb \
txt \
-s6138 \
-odata/extracted_data_fields/education
# ICD 10 main
$file_handlers/ukbconv \
$file_handlers/ukb45020.enc_ukb \
txt \
-s41202 \
-odata/extracted_data_fields/icd_10_main
# ICD 10 secondary
$file_handlers/ukbconv \
$file_handlers/ukb45020.enc_ukb \
txt \
-s41204 \
-odata/extracted_data_fields/icd_10_secondary
# Assessment center
$file_handlers/ukbconv \
$file_handlers/ukb45020.enc_ukb \
txt \
-s54 \
-odata/extracted_data_fields/assessment_center