-
Notifications
You must be signed in to change notification settings - Fork 0
/
3.1_run_ANNOVAR.sh
96 lines (63 loc) · 7.32 KB
/
3.1_run_ANNOVAR.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
#!/bin/bash
##############################################################################################
## Run ANNOVAR to annotate and functionally predict UGT missense variants
##############################################################################################
#-------------------------------------------------------------------------------
# gnomAD v2.1.1 missense variants (GRCh37)
#-------------------------------------------------------------------------------
## Delete " " from Ref and Obs columns
sed 's/'\"'/''/g' input_data/UGT1A1_input.txt > input_data/UGT1A1_input.txt
## Run ANNOVAR
perl table_annovar.pl input_data/UGT1A1_input.txt humandb/ -buildver hg19 -out output_data/myannoUGT1A1 -remove -protocol refGene,dbnsfp42a,dbnsfp30a -operation g,f,f -nastring . -csvout
sed 's/'\"'/''/g' input_data/UGT1A3_input.txt > input_data/UGT1A3_input.txt
perl table_annovar.pl input_data/UGT1A3_input.txt humandb/ -buildver hg19 -out output_data/myannoUGT1A3 -remove -protocol refGene,dbnsfp42a,dbnsfp30a -operation g,f,f -nastring . -csvout
sed 's/'\"'/''/g' input_data/UGT1A4_input.txt > input_data/UGT1A4_input.txt
perl table_annovar.pl input_data/UGT1A4_input.txt humandb/ -buildver hg19 -out output_data/myannoUGT1A4 -remove -protocol refGene,dbnsfp42a,dbnsfp30a -operation g,f,f -nastring . -csvout
sed 's/'\"'/''/g' input_data/UGT1A5_input.txt > input_data/UGT1A5_input.txt
perl table_annovar.pl input_data/UGT1A5_input.txt humandb/ -buildver hg19 -out output_data/myannoUGT1A5 -remove -protocol refGene,dbnsfp42a,dbnsfp30a -operation g,f,f -nastring . -csvout
sed 's/'\"'/''/g' input_data/UGT1A6_input.txt > input_data/UGT1A6_input.txt
perl table_annovar.pl input_data/UGT1A6_input.txt humandb/ -buildver hg19 -out output_data/myannoUGT1A6 -remove -protocol refGene,dbnsfp42a,dbnsfp30a -operation g,f,f -nastring . -csvout
sed 's/'\"'/''/g' input_data/UGT1A7_input.txt > input_data/UGT1A7_input.txt
perl table_annovar.pl input_data/UGT1A7_input.txt humandb/ -buildver hg19 -out output_data/myannoUGT1A7 -remove -protocol refGene,dbnsfp42a,dbnsfp30a -operation g,f,f -nastring . -csvout
sed 's/'\"'/''/g' input_data/UGT1A8_input.txt > input_data/UGT1A8_input.txt
perl table_annovar.pl input_data/UGT1A8_input.txt humandb/ -buildver hg19 -out output_data/myannoUGT1A8 -remove -protocol refGene,dbnsfp42a,dbnsfp30a -operation g,f,f -nastring . -csvout
sed 's/'\"'/''/g' input_data/UGT1A9_input.txt > input_data/UGT1A9_input.txt
perl table_annovar.pl input_data/UGT1A9_input.txt humandb/ -buildver hg19 -out output_data/myannoUGT1A9 -remove -protocol refGene,dbnsfp42a,dbnsfp30a -operation g,f,f -nastring . -csvout
sed 's/'\"'/''/g' input_data/UGT1A10_input.txt > input_data/UGT1A10_input.txt
perl table_annovar.pl input_data/UGT1A10_input.txt humandb/ -buildver hg19 -out output_data/myannoUGT1A10 -remove -protocol refGene,dbnsfp42a,dbnsfp30a -operation g,f,f -nastring . -csvout
sed 's/'\"'/''/g' input_data/UGT2A1_input.txt > input_data/UGT2A1_input.txt
perl table_annovar.pl input_data/UGT2A1_input.txt humandb/ -buildver hg19 -out output_data/myannoUGT2A1 -remove -protocol refGene,dbnsfp42a,dbnsfp30a -operation g,f,f -nastring . -csvout
sed 's/'\"'/''/g' input_data/UGT2A2_input.txt > input_data/UGT2A2_input.txt
perl table_annovar.pl input_data/UGT2A2_input.txt humandb/ -buildver hg19 -out output_data/myannoUGT2A2 -remove -protocol refGene,dbnsfp42a,dbnsfp30a -operation g,f,f -nastring . -csvout
sed 's/'\"'/''/g' input_data/UGT2A3_input.txt > input_data/UGT2A3_input.txt
perl table_annovar.pl input_data/UGT2A3_input.txt humandb/ -buildver hg19 -out output_data/myannoUGT2A3 -remove -protocol refGene,dbnsfp42a,dbnsfp30a -operation g,f,f -nastring . -csvout
sed 's/'\"'/''/g' input_data/UGT2B4_input.txt > input_data/UGT2B4_input.txt
perl table_annovar.pl input_data/UGT2B4_input.txt humandb/ -buildver hg19 -out output_data/myannoUGT2B4 -remove -protocol refGene,dbnsfp42a,dbnsfp30a -operation g,f,f -nastring . -csvout
sed 's/'\"'/''/g' input_data/UGT2B7_input.txt > input_data/UGT2B7_input.txt
perl table_annovar.pl input_data/UGT2B7_input.txt humandb/ -buildver hg19 -out output_data/myannoUGT2B7 -remove -protocol refGene,dbnsfp42a,dbnsfp30a -operation g,f,f -nastring . -csvout
sed 's/'\"'/''/g' input_data/UGT2B10_input.txt > input_data/UGT2B10_input.txt
perl table_annovar.pl input_data/UGT2B10_input.txt humandb/ -buildver hg19 -out output_data/myannoUGT2B10 -remove -protocol refGene,dbnsfp42a,dbnsfp30a -operation g,f,f -nastring . -csvout
sed 's/'\"'/''/g' input_data/UGT2B11_input.txt > input_data/UGT2B11_input.txt
perl table_annovar.pl input_data/UGT2B11_input.txt humandb/ -buildver hg19 -out output_data/myannoUGT2B11 -remove -protocol refGene,dbnsfp42a,dbnsfp30a -operation g,f,f -nastring . -csvout
sed 's/'\"'/''/g' input_data/UGT2B15_input.txt > input_data/UGT2B15_input.txt
perl table_annovar.pl input_data/UGT2B15_input.txt humandb/ -buildver hg19 -out output_data/myannoUGT2B15 -remove -protocol refGene,dbnsfp42a,dbnsfp30a -operation g,f,f -nastring . -csvout
sed 's/'\"'/''/g' input_data/UGT2B17_input.txt > input_data/UGT2B17_input.txt
perl table_annovar.pl input_data/UGT2B17_input.txt humandb/ -buildver hg19 -out output_data/myannoUGT2B17 -remove -protocol refGene,dbnsfp42a,dbnsfp30a -operation g,f,f -nastring . -csvout
sed 's/'\"'/''/g' input_data/UGT2B28_input.txt > input_data/UGT2B28_input.txt
perl table_annovar.pl input_data/UGT2B28_input.txt humandb/ -buildver hg19 -out output_data/myannoUGT2B28 -remove -protocol refGene,dbnsfp42a,dbnsfp30a -operation g,f,f -nastring . -csvout
sed 's/'\"'/''/g' input_data/UGT3A1_input.txt > input_data/UGT3A1_input.txt
perl table_annovar.pl input_data/UGT3A1_input.txt humandb/ -buildver hg19 -out output_data/myannoUGT3A1 -remove -protocol refGene,dbnsfp42a,dbnsfp30a -operation g,f,f -nastring . -csvout
sed 's/'\"'/''/g' input_data/UGT3A2_input.txt > input_data/UGT3A2_input.txt
perl table_annovar.pl input_data/UGT3A2_input.txt humandb/ -buildver hg19 -out output_data/output_data/myannoUGT3A2 -remove -protocol refGene,dbnsfp42a,dbnsfp30a -operation g,f,f -nastring . -csvout
sed 's/'\"'/''/g' input_data/UGT8_input.txt > input_data/UGT8_input.txt
perl table_annovar.pl input_data/UGT8_input.txt humandb/ -buildver hg19 -out output_data/output_data/myannoUGT8 -remove -protocol refGene,dbnsfp42a,dbnsfp30a -operation g,f,f -nastring . -csvout
#-------------------------------------------------------------------------------
# ClinVar missense variants (GRCh37)
#-------------------------------------------------------------------------------
sed 's/'\"'/''/g' input_data/benchmark.txt > input_data/benchmark.txt
perl table_annovar.pl input_data/benchmark.txt humandb/ -buildver hg19 -out output_data/output_data/myanno_benchmark -remove -protocol refGene,dbnsfp42a,dbnsfp30a -operation g,f,f -nastring . -csvout
#-------------------------------------------------------------------------------
# Non-minor variants for all genes (GRCh37)
#-------------------------------------------------------------------------------
sed 's/'\"'/''/g' input_data/non_minor_alleles_allGenes_ANNOVAR_format.txt > input_data/non_minor_alleles_allGenes_ANNOVAR_format.txt
perl table_annovar.pl input_data/non_minor_alleles_allGenes_ANNOVAR_format.txt humandb/ -buildver hg19 -out output_data/output_data/myanno_non_minor -remove -protocol refGene,dbnsfp42a,dbnsfp30a -operation g,f,f -nastring . -csvout