-
Notifications
You must be signed in to change notification settings - Fork 0
/
Copy pathmethylation workflow postproc.dot
164 lines (83 loc) · 7.43 KB
/
methylation workflow postproc.dot
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
digraph workflow {
"BAMPROC_1a" -> "unfiltered methyl calls bedGraph" [label="from BAM processing", style=dotted];
"BAMPROC_2a" -> "unfiltered clinvar methylation call data" [label="from BAM processing", style=dotted];
"BAMPROC_4a" -> "unfiltered mixed methylation calls" [label="from BAM processing", style=dotted];
"BAMPROC_5" -> "ClinVar regions" [label="from preprocessing", style=dotted];
"BAMPROC_6" -> "low map. ClinVar regions" [label="from preprocessing", style=dotted];
"BAMPROC_7a" -> "unfiltered low map. methylation call data" [label="from BAM processing", style=dotted];
"BAMPROC_8a" -> "unfiltered low map. clinvar methylation call data" [label="from BAM processing", style=dotted];
"BAMPROC_1a" [style=invis];
"BAMPROC_2a" [style=invis];
"BAMPROC_4a" [style=invis];
"BAMPROC_5" [style=invis];
"BAMPROC_6" [style=invis];
"BAMPROC_7a" [style=invis];
"BAMPROC_8a" [style=invis];
"BAMPROC_1b" -> "filtered methyl calls bedGraph" [label="from BAM processing", style=dotted];
"BAMPROC_2b" -> "filtered clinvar methylation call data" [label="from BAM processing", style=dotted];
"BAMPROC_3b" -> "filtered pure methylation calls" [label="from BAM processing", style=dotted];
"BAMPROC_7b" -> "filtered low map. methylation call data" [label="from BAM processing", style=dotted];
"BAMPROC_8b" -> "filtered low map. clinvar methylation call data" [label="from BAM processing", style=dotted];
"BAMPROC_1b" [style=invis];
"BAMPROC_2b" [style=invis];
"BAMPROC_3b" [style=invis];
"BAMPROC_7b" [style=invis];
"BAMPROC_8b" [style=invis];
"bedtools intersect -v_1" [shape=diamond, color=gray85, style=filled, label="bedtools intersect -sorted -v \n-a <unfilt.> -b <filt.> | cut -f 1-10,12"];
"bedtools intersect -v_2" [shape=diamond, color=gray85, style=filled, label="bedtools intersect -sorted -v \n-a <unfilt.> -b <filt.> | cut -f 1-10,12"];
"bedtools intersect -wa_wb_3" [shape=diamond, color=gray85, style=filled, label="bedtools intersect -sorted -wa -wb\n -a <unfilt. mixed> -b <filt. pure> | cut -f 1-6,16-24"];
"bedtools intersect -wa_4" [shape=diamond, color=gray85, style=filled, label="bedtools intersect -wa -sorted \n-a <clinvar> -b <miscalls>"];
"bedtools intersect -wa_5" [shape=diamond, color=gray85, style=filled, label="bedtools intersect -wa -sorted \n-a <clinvar> -b <miscalls>"];
"bedtools intersect -wa_6" [shape=diamond, color=gray85, style=filled, label="bedtools intersect -wa -sorted \n-a <clinvar> -b <miscalls>"];
"bedtools intersect -v_7" [shape=diamond, color=gray85, style=filled, label="bedtools intersect -sorted -v \n-a <unfilt.> -b <filt.> | cut -f 1-10,12"];
"bedtools intersect -v_8" [shape=diamond, color=gray85, style=filled, label="bedtools intersect -sorted -v \n-a <unfilt.> -b <filt.> | cut -f 1-10,12"];
"bedtools intersect -v_9" [shape=diamond, color=gray85, style=filled, label="bedtools intersect -sorted -v \n-a <unfilt.> -b <filt.>"];
"unfiltered methyl calls bedGraph" -> "bedtools intersect -v_1" [label="unfiltered"];
"filtered methyl calls bedGraph" -> "bedtools intersect -v_1" [label="filtered"];
"unfiltered clinvar methylation call data" -> "bedtools intersect -v_2" [label="unfiltered"];
"filtered clinvar methylation call data" -> "bedtools intersect -v_2" [label="filtered"];
"unfiltered mixed methylation calls" -> "bedtools intersect -wa_wb_3" [label="unfiltered"];
"filtered pure methylation calls" -> "bedtools intersect -wa_wb_3" [label="filtered"];
"unfiltered low map. methylation call data" -> "bedtools intersect -v_7" [label="unfiltered"];
"filtered low map. methylation call data" -> "bedtools intersect -v_7" [label="filtered"];
"unfiltered low map. clinvar methylation call data" -> "bedtools intersect -v_8" [label="unfiltered"];
"filtered low map. clinvar methylation call data" -> "bedtools intersect -v_8" [label="filtered"];
"bedtools intersect -v_1" -> "miscalled methyl calls bedGraph";
"bedtools intersect -v_2" -> "miscalled clinvar methylation call data";
"bedtools intersect -wa_wb_3" -> "resolved methylation calls";
"bedtools intersect -v_7" -> "miscalled low map. methylation call data";
"bedtools intersect -v_8" -> "miscalled low map. clinvar methylation call data";
"miscalled methyl calls bedGraph" -> "bedtools intersect -wa_5" [label="miscalls"];
"miscalled low map. methylation call data" -> "bedtools intersect -wa_6" [label="miscalls"];
"ClinVar regions" -> "bedtools intersect -wa_5" [label="clinvar"];
"low map. ClinVar regions" -> "bedtools intersect -wa_6" [label="clinvar"];
"bedtools intersect -wa_5" -> "ClinVar regions with methylation miscalls\nwith duplicates";
"bedtools intersect -wa_6" -> "low map. ClinVar regions with methylation miscalls\nwith duplicates";
"ClinVar regions with methylation miscalls\nwith duplicates" -> "ClinVar regions with count of methylation miscalls" [label="count_calls.py"];
"low map. ClinVar regions with methylation miscalls\nwith duplicates" -> "low map. ClinVar regions with count of methylation miscalls" [label="count_calls.py"];
"miscalled methyl calls bedGraph" -> "bedtools intersect -v_9" [label="miscalled"];
"unfiltered low map. methylation call data" -> "bedtools intersect -v_9" [label="unfiltered"];
"bedtools intersect -v_9" -> "underfiltered methylation calls";
"resolved methylation calls" -> "bedtools intersect -wa_4" [label="resolved"];
"ClinVar regions" -> "bedtools intersect -wa_4" [label="clinvar"];
"bedtools intersect -wa_4" -> "ClinVar regions with resolved calls\nwith duplicates";
"ClinVar regions with resolved calls\nwith duplicates" -> "ClinVar regions with count of resolved calls" [label="count_calls.py"];
"ClinVar regions with count of resolved calls" -> "ClinVar regions with count of resolved calls with params" [label="add_params.py"];
"low map. ClinVar regions with count of methylation miscalls" -> "low map. ClinVar regions with count of methylation miscalls with params" [label="add_params.py"];
"ClinVar regions with count of methylation miscalls" -> "ClinVar regions with count of methylation miscalls with params" [label="add_params.py"];
"underfiltered methylation calls" -> "underfiltered methylation calls with params" [label="add_params.py"];
"miscalled clinvar methylation call data" -> "miscalled clinvar methylation call data with params" [label="add_params.py"];
"miscalled low map. clinvar methylation call data" -> "miscalled low map. clinvar methylation call data with params" [label="add_params.py"];
"miscalled low map. methylation call data" -> "miscalled low map. methylation call data with params" [label="add_params.py"];
"miscalled methyl calls bedGraph" -> "miscalled methyl calls bedGraph with params" [label="add_params.py"];
"resolved methylation calls" -> "resolved methylation calls with params" [label="add_params.py"];
"ClinVar regions with count of resolved calls with params" [shape=parallelogram];
"low map. ClinVar regions with count of methylation miscalls with params" [shape=parallelogram];
"ClinVar regions with count of methylation miscalls with params" [shape=parallelogram];
"underfiltered methylation calls with params" [shape=parallelogram];
"miscalled clinvar methylation call data with params" [shape=parallelogram];
"miscalled low map. clinvar methylation call data with params" [shape=parallelogram];
"miscalled low map. methylation call data with params" [shape=parallelogram];
"miscalled methyl calls bedGraph with params" [shape=parallelogram];
"resolved methylation calls with params" [shape=parallelogram];
}