-
Notifications
You must be signed in to change notification settings - Fork 7
/
Copy pathgwastoolkit.regenie.qc.sh
executable file
·190 lines (178 loc) · 8.32 KB
/
gwastoolkit.regenie.qc.sh
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
#!/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