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calc_pca_full.sh
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calc_pca_full.sh
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#!/bin/bash
set -e
source constants_.sh
source parse_args.sh "$@"
# Parse input
target_dataset="${datasets_path}${target}/${imp}/"
if [[ -z ${maf} ]]; then maf=0.05; fi
if [[ -z ${geno} ]]; then geno=0.1; fi
if [[ -z ${imp} ]]; then imp="original"; fi
if [[ -z ${memory} ]]; then memory=500000; fi
if [[ -z ${threads} ]]; then threads=80; fi
if [[ -z ${stage} ]]; then stage=2; fi
# Start pipeline
if [[ ${stage} -le 1 ]]; then
echo '### QC ###'
plink \
--bfile ${target_dataset}ds \
--keep "${datasets_path}${target}/pop.panel" \
--out ${target_dataset}ds.QC \
--memory ${memory} \
--threads ${threads} \
--maf ${maf} \
--geno ${geno} \
--hwe 1e-6 \
--make-bed
fi
if [[ ${stage} -le 2 ]]; then
echo '### perform prunning ###'
plink \
--bfile ${target_dataset}ds.QC \
--out ${target_dataset}ds \
--memory ${memory} \
--threads ${threads} \
--indep-pairwise 200 50 0.25
fi
if [[ ${stage} -le 3 ]]; then
echo '### calculate the first 6 PCs ###'
plink \
--bfile ${target_dataset}ds.QC \
--out ${target_dataset}ds \
--memory ${memory} \
--threads ${threads} \
--extract ${target_dataset}ds.prune.in \
--pca 200
fi