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comparison test-data/varcalling.outdir/mutation_inspector.json @ 3:b591b35283e4 draft default tip

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author trinity_ctat
date Wed, 14 Nov 2018 12:34:06 -0500
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2:c15d9049ab81 3:b591b35283e4
1 {
2 "BAM": "/broad/hptmp/bankapur/full_mut/varcalling.outdir/misc/recalibrated.bam",
3 "BAM_INDEX": "/broad/hptmp/bankapur/full_mut/varcalling.outdir/misc/recalibrated.bai",
4 "BED": "/seq/regev_genome_portal/RESOURCES/CTAT_GENOME_LIB/GRCh38_v27_CTAT_lib_Feb092018/ctat_genome_lib_build_dir/ctat_mutation_lib/refGene.sort.bed",
5 "BED_INDEX": "/seq/regev_genome_portal/RESOURCES/CTAT_GENOME_LIB/GRCh38_v27_CTAT_lib_Feb092018/ctat_genome_lib_build_dir/ctat_mutation_lib/refGene.sort.bed.idx",
6 "SAMPLE": "varcalling.outdir",
7 "SNV": [
8 {
9 "ALT": "G",
10 "CHASM_FDR": "0.2",
11 "CHASM_PVALUE": "0.1114",
12 "CHROM": "chr5",
13 "COSMIC_ID": "COSM4006021",
14 "DP": "4",
15 "GENE": "LOC100288152,SLC9A3",
16 "KGPROD": "NA",
17 "MQ": "60",
18 "NSF": "NA",
19 "NSM": "NA",
20 "NSN": "NA",
21 "PMC": "NA",
22 "POS": "474989",
23 "QUAL": "96.03",
24 "REF": "A",
25 "RS": "NA",
26 "SAO": "NA",
27 "TISSUE": "urinary_tract",
28 "TUMOR": "carcinoma_--_NS",
29 "VEST_FDR": "1",
30 "VEST_PVALUE": "0.96802"
31 },
32 {
33 "ALT": "A",
34 "CHASM_FDR": "0.15",
35 "CHASM_PVALUE": "0.0694",
36 "CHROM": "chr5",
37 "COSMIC_ID": "NA",
38 "DP": "45",
39 "GENE": "TRIM41",
40 "KGPROD": "NA",
41 "MQ": "60",
42 "NSF": "NA",
43 "NSM": "NA",
44 "NSN": "NA",
45 "PMC": "NA",
46 "POS": "181224474",
47 "QUAL": "349.77",
48 "REF": "G",
49 "RS": "NA",
50 "SAO": "NA",
51 "TISSUE": "NA",
52 "TUMOR": "NA",
53 "VEST_FDR": "1",
54 "VEST_PVALUE": "0.48052"
55 },
56 {
57 "ALT": "A",
58 "CHASM_FDR": "0.1",
59 "CHASM_PVALUE": "0.0344",
60 "CHROM": "chr8",
61 "COSMIC_ID": "COSM3750086",
62 "DP": "66",
63 "GENE": "PLEC",
64 "KGPROD": "NA",
65 "MQ": "60",
66 "NSF": "NA",
67 "NSM": "NA",
68 "NSN": "NA",
69 "PMC": "NA",
70 "POS": "143923759",
71 "QUAL": "838.77",
72 "REF": "G",
73 "RS": "NA",
74 "SAO": "NA",
75 "TISSUE": "large_intestine",
76 "TUMOR": "carcinoma_--_adenocarcinoma",
77 "VEST_FDR": "1",
78 "VEST_PVALUE": "0.84202"
79 },
80 {
81 "ALT": "A",
82 "CHASM_FDR": "0.15",
83 "CHASM_PVALUE": "0.0744",
84 "CHROM": "chr12",
85 "COSMIC_ID": "COSM3753397",
86 "DP": "48",
87 "GENE": "TIMELESS",
88 "KGPROD": "NA",
89 "MQ": "60",
90 "NSF": "NA",
91 "NSM": "NA",
92 "NSN": "NA",
93 "PMC": "NA",
94 "POS": "56420869",
95 "QUAL": "384.77",
96 "REF": "G",
97 "RS": "NA",
98 "SAO": "NA",
99 "TISSUE": "large_intestine",
100 "TUMOR": "carcinoma_--_adenocarcinoma",
101 "VEST_FDR": "0.95",
102 "VEST_PVALUE": "0.18439"
103 },
104 {
105 "ALT": "T",
106 "CHASM_FDR": "0.05",
107 "CHASM_PVALUE": "0",
108 "CHROM": "chr17",
109 "COSMIC_ID": "COSM3717625",
110 "DP": "61",
111 "GENE": "TP53",
112 "KGPROD": "NA",
113 "MQ": "60",
114 "NSF": "NA",
115 "NSM": "NA",
116 "NSN": "NA",
117 "PMC": "NA",
118 "POS": "7673767",
119 "QUAL": "1848.77",
120 "REF": "C",
121 "RS": "NA",
122 "SAO": "NA",
123 "TISSUE": "bone",
124 "TUMOR": "Ewings_sarcoma-peripheral_primitive_neuroectodermal_tumour_--_NS",
125 "VEST_FDR": "0.15",
126 "VEST_PVALUE": "0.01447"
127 },
128 {
129 "ALT": "C",
130 "CHASM_FDR": "0.15",
131 "CHASM_PVALUE": "0.087",
132 "CHROM": "chr17",
133 "COSMIC_ID": "COSM3766193",
134 "DP": "80",
135 "GENE": "TP53",
136 "KGPROD": "NA",
137 "MQ": "60",
138 "NSF": "NA",
139 "NSM": "NA",
140 "NSN": "NA",
141 "PMC": "NA",
142 "POS": "7676154",
143 "QUAL": "2161.77",
144 "REF": "G",
145 "RS": "NA",
146 "SAO": "NA",
147 "TISSUE": "haematopoietic_and_lymphoid_tissue",
148 "TUMOR": "haematopoietic_neoplasm_--_acute_myeloid_leukaemia",
149 "VEST_FDR": "1",
150 "VEST_PVALUE": "0.52717"
151 },
152 {
153 "ALT": "C",
154 "CHASM_FDR": "0.1",
155 "CHASM_PVALUE": "0.0372",
156 "CHROM": "chr17",
157 "COSMIC_ID": "COSM3755560",
158 "DP": "4",
159 "GENE": "BRCA1",
160 "KGPROD": "NA",
161 "MQ": "60",
162 "NSF": "NA",
163 "NSM": "NA",
164 "NSN": "NA",
165 "PMC": "NA",
166 "POS": "43071077",
167 "QUAL": "92.03",
168 "REF": "T",
169 "RS": "NA",
170 "SAO": "NA",
171 "TISSUE": "haematopoietic_and_lymphoid_tissue",
172 "TUMOR": "haematopoietic_neoplasm_--_acute_myeloid_leukaemia",
173 "VEST_FDR": "1",
174 "VEST_PVALUE": "0.3446"
175 },
176 {
177 "ALT": "C",
178 "CHASM_FDR": "0.05",
179 "CHASM_PVALUE": "0.0002",
180 "CHROM": "chr17",
181 "COSMIC_ID": "COSM3755561",
182 "DP": "4",
183 "GENE": "BRCA1",
184 "KGPROD": "NA",
185 "MQ": "60",
186 "NSF": "NA",
187 "NSM": "NA",
188 "NSN": "NA",
189 "PMC": "NA",
190 "POS": "43091983",
191 "QUAL": "84.03",
192 "REF": "T",
193 "RS": "NA",
194 "SAO": "NA",
195 "TISSUE": "soft_tissue",
196 "TUMOR": "haemangioblastoma_--_NS",
197 "VEST_FDR": "1",
198 "VEST_PVALUE": "0.64447"
199 },
200 {
201 "ALT": "A",
202 "CHASM_FDR": "0.05",
203 "CHASM_PVALUE": "0.0004",
204 "CHROM": "chr17",
205 "COSMIC_ID": "COSM3755564",
206 "DP": "2",
207 "GENE": "BRCA1",
208 "KGPROD": "NA",
209 "MQ": "60",
210 "NSF": "NA",
211 "NSM": "NA",
212 "NSN": "NA",
213 "PMC": "NA",
214 "POS": "43092919",
215 "QUAL": "33.74",
216 "REF": "G",
217 "RS": "NA",
218 "SAO": "NA",
219 "TISSUE": "prostate",
220 "TUMOR": "carcinoma_--_NS",
221 "VEST_FDR": "1",
222 "VEST_PVALUE": "0.33539"
223 },
224 {
225 "ALT": "T",
226 "CHASM_FDR": "0.05",
227 "CHASM_PVALUE": "0.0014",
228 "CHROM": "chr17",
229 "COSMIC_ID": "COSM4989394",
230 "DP": "11",
231 "GENE": "BRCA1",
232 "KGPROD": "NA",
233 "MQ": "60",
234 "NSF": "NA",
235 "NSM": "NA",
236 "NSN": "NA",
237 "PMC": "NA",
238 "POS": "43093454",
239 "QUAL": "425.77",
240 "REF": "C",
241 "RS": "NA",
242 "SAO": "NA",
243 "TISSUE": "soft_tissue",
244 "TUMOR": "rhabdomyosarcoma_--_embryonal",
245 "VEST_FDR": "1",
246 "VEST_PVALUE": "0.51068"
247 },
248 {
249 "ALT": "C",
250 "CHASM_FDR": "0.05",
251 "CHASM_PVALUE": "0.0004",
252 "CHROM": "chr19",
253 "COSMIC_ID": "NA",
254 "DP": "106",
255 "GENE": "PAK4",
256 "KGPROD": "NA",
257 "MQ": "60",
258 "NSF": "NA",
259 "NSM": "NA",
260 "NSN": "NA",
261 "PMC": "NA",
262 "POS": "39177761",
263 "QUAL": "1134.77",
264 "REF": "G",
265 "RS": "NA",
266 "SAO": "NA",
267 "TISSUE": "NA",
268 "TUMOR": "NA",
269 "VEST_FDR": "0.15",
270 "VEST_PVALUE": "0.01093"
271 },
272 {
273 "ALT": "C",
274 "CHASM_FDR": "0.15",
275 "CHASM_PVALUE": "0.093",
276 "CHROM": "chr19",
277 "COSMIC_ID": "COSM3721172",
278 "DP": "12",
279 "GENE": "CCDC9",
280 "KGPROD": "NA",
281 "MQ": "60",
282 "NSF": "NA",
283 "NSM": "NA",
284 "NSN": "NA",
285 "PMC": "NA",
286 "POS": "47271515",
287 "QUAL": "336.77",
288 "REF": "T",
289 "RS": "NA",
290 "SAO": "NA",
291 "TISSUE": "haematopoietic_and_lymphoid_tissue",
292 "TUMOR": "haematopoietic_neoplasm_--_acute_myeloid_leukaemia",
293 "VEST_FDR": "1",
294 "VEST_PVALUE": "0.97622"
295 },
296 {
297 "ALT": "T",
298 "CHASM_FDR": "0.15",
299 "CHASM_PVALUE": "0.0834",
300 "CHROM": "chr20",
301 "COSMIC_ID": "COSM3758608",
302 "DP": "26",
303 "GENE": "TP53RK",
304 "KGPROD": "NA",
305 "MQ": "60",
306 "NSF": "NA",
307 "NSM": "NA",
308 "NSN": "NA",
309 "PMC": "NA",
310 "POS": "46687147",
311 "QUAL": "423.77",
312 "REF": "C",
313 "RS": "NA",
314 "SAO": "NA",
315 "TISSUE": "pancreas",
316 "TUMOR": "carcinoma_--_ductal_carcinoma",
317 "VEST_FDR": "1",
318 "VEST_PVALUE": "0.88584"
319 }
320 ]
321 }