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Merge pull request #15 from swvanderlaan/dev_regenie
Add basic REGENIE to GWASToolkit
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,190 @@ | ||
| #!/bin/bash | ||
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| ### 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' | ||
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| RED='\033[01;31m' | ||
| GREEN='\033[01;32m' | ||
| YELLOW='\033[01;33m' | ||
| PURPLE='\033[01;35m' | ||
| CYAN='\033[01;36m' | ||
| WHITE='\033[01;37m' | ||
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| 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}" | ||
| } | ||
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| ### 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 | ||
| } | ||
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| 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 "+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++" | ||
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| ### LOADING CONFIGURATION FILE | ||
| source "$1" # Depends on arg1. | ||
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| ### REQUIRED | GENERALS | ||
| CONFIGURATIONFILE="$1" # Depends on arg1 -- but also on where it resides!!! | ||
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| ### 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 | ||
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| 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 | ||
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| 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 | ||
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| 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 | ||
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| # script_copyright_message |
Oops, something went wrong.