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gwastoolkit.regenie.qc.sh
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gwastoolkit.regenie.qc.sh
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#!/bin/bash
### Creating display functions
### Setting colouring
NONE='\033[00m'
OPAQUE='\033[2m'
FLASHING='\033[5m'
BOLD='\033[1m'
ITALIC='\033[3m'
UNDERLINE='\033[4m'
STRIKETHROUGH='\033[9m'
RED='\033[01;31m'
GREEN='\033[01;32m'
YELLOW='\033[01;33m'
PURPLE='\033[01;35m'
CYAN='\033[01;36m'
WHITE='\033[01;37m'
function echobold { #'echobold' is the function name
echo -e "${BOLD}${1}${NONE}" # this is whatever the function needs to execute, note ${1} is the text for echo
}
function echoitalic {
echo -e "${ITALIC}${1}${NONE}"
}
function echonooption {
echo -e "${OPAQUE}${RED}${1}${NONE}"
}
function echoerrorflash {
echo -e "${RED}${BOLD}${FLASHING}${1}${NONE}"
}
function echoerror {
echo -e "${RED}${1}${NONE}"
}
# errors no option
function echoerrornooption {
echo -e "${YELLOW}${1}${NONE}"
}
function echoerrorflashnooption {
echo -e "${YELLOW}${BOLD}${FLASHING}${1}${NONE}"
}
### MESSAGE FUNCTIONS
script_copyright_message() {
echo ""
THISYEAR=$(date +'%Y')
echo "+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++"
echo "+ The MIT License (MIT) +"
echo "+ Copyright (c) 2015-${THISYEAR} Tim S. Peters +"
echo "+ +"
echo "+ Permission is hereby granted, free of charge, to any person obtaining a copy of this software and +"
echo "+ associated documentation files (the \"Software\"), to deal in the Software without restriction, +"
echo "+ including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, +"
echo "+ and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, +"
echo "+ subject to the following conditions: +"
echo "+ +"
echo "+ The above copyright notice and this permission notice shall be included in all copies or substantial +"
echo "+ portions of the Software. +"
echo "+ +"
echo "+ THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT +"
echo "+ NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND +"
echo "+ NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES +"
echo "+ OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN +"
echo "+ CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. +"
echo "+ +"
echo "+ Reference: http://opensource.org. +"
echo "+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++"
}
script_arguments_error() {
echoerror "$1" # ERROR MESSAGE
echoerror ""
echoerror "- Argument #1 is path_to the configuration file."
echoerror ""
echoerror "An example command would be: gwastoolkit.regenie.qc.sh [arg1: path_to_configuration_file]"
echoerror ""
echoerror "+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++"
# The wrong arguments are passed, so we'll exit the script now!
exit 1
}
echobold "+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++"
echobold " GWASTOOLKIT QUALITY CONTROL for REGENIE"
echobold " quality control of REGENIE analysis results"
echobold ""
echobold " Version : v1.0.0"
echobold ""
echobold " Last update: 2024-08-29"
echobold " Written by : Tim S. Peters ([email protected])."
echobold ""
echobold " Testers: - "
echobold ""
echobold " Description: Quality control of a REGENIE analysis:"
echobold " Filter on: - autosome snps"
echobold " - MAF"
echobold " - MAC"
echobold " - call rate"
echobold " - Hardy-Weinberg Equilibrium (HWE) p-value"
echobold " - LD r^2"
echobold " - exclude problamatic SNPs in long-range LD regions"
echobold ""
echobold "+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++"
### LOADING CONFIGURATION FILE
source "$1" # Depends on arg1.
### REQUIRED | GENERALS
CONFIGURATIONFILE="$1" # Depends on arg1 -- but also on where it resides!!!
### START of if-else statement for the number of command-line arguments passed ###
if [[ $# -lt 1 ]]; then
echo "Oh, computer says no! Number of arguments found "$#"."
script_arguments_error "You must supply [1] argument for cleaning of *** GENOME-WIDE ANALYSIS *** results!"
script_copyright_message
else
### Make and/or set the output directory
if [ ! -d ${PROJECTDIR}/${PROJECTNAME}/regenie_results ]; then
echo "The output directory does not exist. Making and setting it."
mkdir -v ${PROJECTDIR}/${PROJECTNAME}/regenie_results
OUTPUT_DIR=${PROJECTDIR}/${PROJECTNAME}/regenie_results
else
echo "The output directory already exists. Setting it."
OUTPUT_DIR=${PROJECTDIR}/${PROJECTNAME}/regenie_results
fi
if [ ! -d ${OUTPUT_DIR}/pre_processing ]; then
echo "The QC output directory does not exist. Making and setting it."
mkdir -v ${OUTPUT_DIR}/pre_processing
QC_OUTPUT_DIR=${OUTPUT_DIR}/pre_processing
else
echo "The QC output directory already exists. Setting it."
QC_OUTPUT_DIR=${OUTPUT_DIR}/pre_processing
fi
echo "All arguments are passed. These are the settings:"
echo "The output directory is...................: ${OUTPUT_DIR}"
echo "The call rate filter is...................: ${REGENIE_CALL_RATE}"
echo "The minimum minor allele frequency is.....: ${REGENIE_MAF}"
echo "The minimum HWE p-value is................: ${REGENIE_HWE}"
echo "The filter for independent SNPs is........: ${REGENIE_PRUNE}"
echo ""
# PLOT GWAS RESULTS
echo "+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++"
echo " STARTING QUALITY CONTROL"
echo ""
echo "Please be patient...this can take a long time depending on the number of files."
echo "We started at: "$(date)
echo ""
echo ""
echo "First, get a list of A/T and C/G SNPs, to exclude later:"
cat ${IMPUTEDDATA_ALLCHR}.pvar | \
awk '($4 == "A" && $5 == "T") || ($4 == "T" && $5 == "A") || ($4 == "C" && $5 == "G") || ($4 == "G" && $5 == "C")' | \
awk '{ print $3, $1, $2, 0, $4, $5 }' > ${QC_OUTPUT_DIR}/all.atcg.variants.txt
echo ""
echo ""
echo "Second, filtering data, using the following criteria: "
echo " * CALL RATE < ${REGENIE_CALL_RATE}"
echo " * MAF >= ${REGENIE_MAF}"
echo " * HWE <= ${REGENIE_HWE}"
echo " * indep_pairwise ${REGENIE_PRUNE}"
$PLINK2 --pfile ${IMPUTEDDATA_ALLCHR} \
--autosome \
--maf ${REGENIE_MAF} --geno ${REGENIE_CALL_RATE} --hwe ${REGENIE_HWE} \
--exclude-if-info "R2>0.99" \
--indep-pairwise ${REGENIE_PRUNE}\
--exclude range ${EXCLUDE_RANGE_FILE} \
--make-pgen --out ${QC_OUTPUT_DIR}/aegscombo_topmed_r3_f10_b38.allChrs.temp
echo ""
echo ""
echo "Third, prune out unwanted SNPs in high LD."
$PLINK2 --pfile ${QC_OUTPUT_DIR}/aegscombo_topmed_r3_f10_b38.allChrs.temp \
--extract ${QC_OUTPUT_DIR}/aegscombo_topmed_r3_f10_b38.allChrs.temp.prune.in \
--make-pgen --out ${QC_OUTPUT_DIR}/aegscombo_topmed_r3_f10_b38.allChrs.ultraclean.temp
echo ""
echo ""
echo "Fourth, remove the A/T and C/G SNPs."
$PLINK2 --pfile ${QC_OUTPUT_DIR}/aegscombo_topmed_r3_f10_b38.allChrs.ultraclean.temp \
--exclude ${QC_OUTPUT_DIR}/all.atcg.variants.txt \
--write-snplist --write-samples --no-id-header \
--make-pgen --out ${QC_OUTPUT_DIR}/aegscombo_topmed_r3_f10_b38.allChrs.QC
echo ""
echo ""
echo "Finishing up..."
rm -fv ${QC_OUTPUT_DIR}/*.temp*
echo ""
echo ""
### END of if-else statement for the number of command-line arguments passed ###
fi
# script_copyright_message