Mercurial > repos > niels > annovar_yaml_wrapper

comparison annovar_yaml/YAML_arguments_annovar.yml @ 5:856448f167da draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author niels
date Mon, 13 May 2019 06:37:39 -0400
parents
children 7f4fb56714e8
comparison
equal deleted inserted replaced
4:0925376a2624 5:856448f167da
1 GENERAL:
2 - APPLICATION: 'annovar'
3 PATHSCRIPTS: '/hpc/cog_bioinf/pathologie/users/snouwens/Annovar_Moldia/Annovar/'
4 CODING_ANNOVAR: 'coding_annovar.pl '
5 TABLE_ANNOVAR: 'table_annovar.pl '
6 LOCATION_DATABASE: '/hpc/cog_bioinf/pathologie/users/snouwens/Annovar_Moldia/Annovar/'
7 DOT2UNDERLINE:
8 yes: '--dot2underline '
9 no: ''
10 NASTRING: '--nastring . '
11 OTHERINFO:
12 yes: '--otherinfo '
13 no: ''
14 POLISH:
15 yes: '--polish '
16 no: ''
17 REMOVE:
18 yes: '--remove '
19 no: ''
20 THREAD: '--thread 8 '
21 INPUTFORMAT:
22 vcfinput: '--vcfinput '
23 SPECIES:
24 human: 'humandb '
25 mouse: 'mousedb '
26 BUILD: '--buildver hg19 '
27 ANALYSIS:
28 DATABASES:
29 - NAME: 'cosmic84'
30 PROTOCOL: 'cosmic'
31 VERSION: '84'
32 COMMENT: '20190221'
33 AVAILABLE:
34 yes: '1'
35 no: '0'
36 REQUIRED:
37 yes: '1'
38 no: '0'
39 OPERATION: 'f'
40 COLSWANTED: '--colswanted 4 '
41 - NAME: 'refgene19'
42 PROTOCOL: 'refgene'
43 VERSION: '19'
44 COMMENT: '20190210'
45 AVAILABLE:
46 yes: '1'
47 no: '0'
48 REQUIRED:
49 yes: '1'
50 no: '0'
51 OPERATION: 'g'
52 HGVS:
53 yes: '--hgvs '
54 no: ''
55 SPLICING: '--splicing 6 '
56 EXONSPLIC:
57 yes: '--exonicsplicing '
58 no: ''
59 - NAME: 'ncbiRefSeq_UMCU'
60 PROTOCOL: 'ncbiRefSeq'
61 VERSION: '_UMCU'
62 AVAILABLE:
63 yes: '1'
64 no: '0'
65 REQUIRED:
66 yes: '1'
67 no: '0'
68 COMMENT: "100519"
69 OPERATION: 'g'
70 HGVS:
71 yes: '--hgvs '
72 no: ''
73 SPLICING: '--splicing 6 '
74 EXONSPLIC:
75 yes: '--exonicsplicing '
76 no: ''
77 - NAME: 'avsnp150'
78 PROTOCOL: 'avsnp'
79 VERSION: '150'
80 AVAILABLE:
81 yes: '1'
82 no: '0'
83 REQUIRED:
84 yes: '1'
85 no: '0'
86 OPERATION: 'f'
87 COLSWANTED: '--colswanted 1 '
88 - NAME: 'clinvar_20180603'
89 PROTOCOL: 'clinvar'
90 VERSION: '_20180603'
91 COMMENT: 'blah'
92 AVAILABLE:
93 yes: '1'
94 no: '0'
95 REQUIRED:
96 yes: '1'
97 no: '0'
98 OPERATION: 'f'
99 COLSWANTED: '--colswanted 5 '
100 - NAME: 'class100519'
101 PROTOCOL: 'class'
102 VERSION: '100519'
103 AVAILABLE:
104 yes: '1'
105 no: '0'
106 REQUIRED:
107 yes: '1'
108 no: '0'
109 OPERATION: 'f'
110 COLSWANTED: '--colswanted 1 '
111