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3
|
1
|
|
0
|
2 <filter>
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3 SNV_FILTER
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4 SNV_FILTER_NUM
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|
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5 CHR
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|
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6 </filter>
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7
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|
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8 <files>
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9 ROOT
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3
|
10 cnv = data/cnv.txt
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|
11 cnvlg = data/cnv.large.scale.txt
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|
12 sv = data/snv.txt
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|
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13 mart = data/biomart.txt
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14 CIRCOS
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|
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15 mask = data/genes_to_hide.txt
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|
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16 genes = data/genes_to_label.txt
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0
|
17 </files>
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|
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18
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3
|
19
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|
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20 <map>
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21 log2 = avg:sprintf("%.2f",2*2**x)
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22 </map>
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23
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|
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24 # 0-indexed column numbers and names
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0
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25 <fields>
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3
|
26 <cnvlg>
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|
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27 key = chr
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28 0 = chr
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|
29 1 = start
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30 2 = end
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31 3 = type:lc
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|
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32 </cnvlg>
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0
|
33 <cnv>
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|
|
34 key = sample,chr
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|
3
|
35 0 = sample
|
|
0
|
36 1 = chr
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|
|
37 2 = start
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|
|
38 3 = end
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|
3
|
39 # :map(x,y) will create a new field x based on intervals defined in a block
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|
|
40 #
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|
|
41 # e.g.
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|
|
42 # value of 2*2**(log2) (see <map> block above) will be used to assign key "category"
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|
|
43 # based on <cnv><log2> intervals
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|
|
44 5 = log2:map(category,cnv/log2)
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|
0
|
45 </cnv>
|
|
|
46 <sv>
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|
|
47 key = id,sample
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|
|
48 4 = chr
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|
|
49 5 = start
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|
|
50 6 = end
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|
|
51 8 = type:lc
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|
|
52 15 = sample
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|
|
53 47 = id
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|
|
54 53 = aa
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|
|
55 </sv>
|
|
|
56 <genes>
|
|
|
57 key = chr
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|
|
58 0 = id
|
|
3
|
59 3 = end
|
|
|
60 2 = start
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|
|
61 1 = chr
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|
|
62 4 = name
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|
0
|
63 </genes>
|
|
|
64 </fields>
|
|
|
65
|
|
|
66 <cnv>
|
|
|
67 filter = yes
|
|
|
68 <types>
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|
|
69 amp = 20
|
|
|
70 gain = 15
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|
|
71 neut = 0
|
|
|
72 hetd = 10
|
|
|
73 homd = 5
|
|
|
74 hlamp = 0
|
|
|
75 </types>
|
|
3
|
76 # assign log2 ranges to CNV event categories
|
|
|
77 #
|
|
|
78 # ( indicates open interval
|
|
|
79 # [ indicates closed interval
|
|
|
80 #
|
|
|
81 # e.g. (1,2] is 1 < x <= 2
|
|
|
82 # [2,3) is 2 <= x < 3
|
|
|
83 #
|
|
|
84 # The intervals must be disjoint and completely cover
|
|
|
85 # all possible values you're going to test.
|
|
|
86 <log2>
|
|
|
87 # max = category
|
|
|
88 (,1) = homd
|
|
|
89 [1,2) = hetd
|
|
|
90 2 = neut
|
|
|
91 (2,3] = gain
|
|
|
92 (3,) = amp
|
|
|
93 </log2>
|
|
0
|
94 </cnv>
|
|
|
95
|
|
|
96 <sv>
|
|
3
|
97 # only pay attention to SV types listed <types>
|
|
0
|
98 filter = yes
|
|
3
|
99 # only consider the most damaging type of mutation in a patient
|
|
|
100 # (one with top score in <types>
|
|
|
101 # the absolute value of the damage weight is unimportant, only order matters
|
|
0
|
102 top_damage_only = yes
|
|
|
103 <types>
|
|
|
104 nonsense_mutation = 35
|
|
|
105 frame_shift_del = 30
|
|
|
106 frame_shift_ins = 25
|
|
|
107 in_frame_del = 20
|
|
|
108 in_frame_ins = 15
|
|
|
109 splice_site = 10
|
|
|
110 nonstop_mutation = 5
|
|
|
111 missense_mutation = 1
|
|
|
112 </types>
|
|
3
|
113 </sv>
|
