This repository has been archived by the owner on Oct 23, 2023. It is now read-only.
-
Notifications
You must be signed in to change notification settings - Fork 0
/
GRCh38.json
executable file
·317 lines (312 loc) · 23.8 KB
/
GRCh38.json
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
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
{"references": {
"exomeseq": {
"BWAGENOME": "/data/CCBR_Pipeliner/db/PipeDB/lib/GRCh38.d1.vd1.fa",
"PON": "/data/CCBR_Pipeliner/db/PipeDB/lib/1kGenomes_ExAC_0.001freq_PON.hg38.vcf.gz",
"GENOME": "/data/CCBR_Pipeliner/db/PipeDB/lib/GRCh38.d1.vd1.fa",
"CNVKITGENOME": "/data/CCBR_Pipeliner/db/PipeDB/lib/GRCh38.d1.vd1.fa",
# "CNVKITREF": "/data/CCBR_Pipeliner/db/PipeDB/lib/GRCh38.d1.vd1_flatRef.cnn",
"CNVKITACCESS": "/data/CCBR_Pipeliner/db/PipeDB/lib/access-5k-mappable.grch38.bed",
"INDELSITES": "/fdb/GATK_resource_bundle/hg38bundle/Mills_and_1000G_gold_standard.indels.hg38.vcf.gz",
# "NOVOINDEX": "/data/CCBR_Pipeliner/db/PipeDB/lib/human_g1k_v37_iupac.nix",
# "REFFLAT": "/data/CCBR_Pipeliner/db/PipeDB/lib/reformatS04380219_qualimap.bed",
"KNOWNANCESTRY": "/data/CCBR_Pipeliner/db/PipeDB/lib/1k_genomes_phase3_autosomes.hg38.vcf.gz",
"ADMIXTUREKEY": "/data/CCBR_Pipeliner/db/PipeDB/lib/1k_genomes_superpop_key.txt",
"ADMIXTUREREFS": "5",
# "KNOWNVCF": "/data/CCBR_Pipeliner/db/PipeDB/lib/1k_genomes_compSet.vcf",
"KNOWNVCF2": "/fdb/GATK_resource_bundle/hg38bundle/1000G_phase1.snps.high_confidence.hg38.vcf.gz",
"SNPSITES": "/fdb/GATK_resource_bundle/hg38bundle/dbsnp_146.hg38.vcf.gz",
"KNOWNINDELS": "-known /fdb/GATK_resource_bundle/hg38bundle/Mills_and_1000G_gold_standard.indels.hg38.vcf.gz -known /data/CCBR_Pipeliner/db/PipeDB/lib/ALL.wgs.1000G_phase3.GRCh38.ncbi_remapper.20150424.shapeit2_indels.vcf.gz",
"KNOWNRECAL": "-knownSites /fdb/GATK_resource_bundle/hg38bundle/dbsnp_138.hg38.vcf.gz -knownSites /fdb/GATK_resource_bundle/hg38bundle/Mills_and_1000G_gold_standard.indels.hg38.vcf.gz -knownSites /data/CCBR_Pipeliner/db/PipeDB/lib/ALL.wgs.1000G_phase3.GRCh38.ncbi_remapper.20150424.shapeit2_indels.vcf.gz",
"THETASNPS": "/data/CCBR_Pipeliner/db/PipeDB/lib/hg38_theta_SNPfile.txt",
"INDELSITES2": "/data/CCBR_Pipeliner/db/PipeDB/lib/ALL.wgs.1000G_phase3.GRCh38.ncbi_remapper.20150424.shapeit2_indels.vcf.gz",
"ALVIEWGENOME": "hg38",
"CONPAIRMARKERSA": "/data/CCBR_Pipeliner/db/PipeDB/lib/hg38.autosomes.phase3_shapeit2_mvncall_integrated.20130502.SNV.genotype.sselect_v4_MAF_0.4_LD_0.8.txt",
"CONPAIRMARKERSB": "/data/CCBR_Pipeliner/db/PipeDB/lib/hg38.autosomes.phase3_shapeit2_mvncall_integrated.20130502.SNV.genotype.sselect_v4_MAF_0.4_LD_0.8.bed",
"EXONS": "/data/CCBR_Pipeliner/db/PipeDB/lib/hg38_exons.bed",
# "ANNDIR": "/data/CCBR_Pipeliner/db/PipeDB/AnnovarDB/",
"STRELKA_CONFIG": "/data/CCBR_Pipeliner/db/PipeDB/lib/strelka_demo_config.ini",
"CNVKIT_TARGETS": "/data/CCBR_Pipeliner/db/PipeDB/lib/human_SSv5_cnvkit_targets.bed",
"CNVKIT_ANTITARGETS": "/data/CCBR_Pipeliner/db/PipeDB/lib/human_SSv5_cnvkit_antitargets.bed",
"DELLY_EXCLUSIONS": "/data/CCBR_Pipeliner/db/PipeDB/lib/delly.human.hg38.excl.tsv",
"FASTQ_SCREEN_CONFIG": "/data/CCBR_Pipeliner/db/PipeDB/lib/fastq_screen.conf",
"tg_GS_INDELS": "/fdb/GATK_resource_bundle/hg38bundle/Mills_and_1000G_gold_standard.indels.hg38.vcf.gz",
"tg_PHASE_INDELS": "/data/CCBR_Pipeliner/db/PipeDB/lib/ALL.wgs.1000G_phase3.GRCh38.ncbi_remapper.20150424.shapeit2_indels.vcf.gz",
"SNP138": "/fdb/GATK_resource_bundle/hg38bundle/dbsnp_138.hg38.vcf.gz",
"HAPMAP": "/fdb/GATK_resource_bundle/hg38bundle/hapmap_3.3.hg38.vcf.gz",
"B1K": "/fdb/GATK_resource_bundle/hg38bundle/1000G_phase1.snps.high_confidence.hg38.vcf.gz",
"OMNI": "/fdb/GATK_resource_bundle/hg38bundle/1000G_omni2.5.hg38.vcf.gz",
"adapter.file": "/data/CCBR_Pipeliner/db/PipeDB/dev/TruSeq_and_nextera_adapters.ngsqc.dat",
"fastqc.adapters": "/data/CCBR_Pipeliner/db/PipeDB/dev/fastqc.adapters",
"trimmomatic.adapters": "/data/CCBR_Pipeliner/db/PipeDB/dev/adapters2.fa",
"ORGANISM": "HUMAN",
"AVIASET": "hg38",
"ADAPTER1": "AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC",
"ADAPTER2": "AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT",
"nextera1": "CTGTCTCTTATACACATCTCCGAGCCCACGAGAC",
"nextera2": "CTGTCTCTTATACACATCTGACGCTGCCGACGA",
# "DB29": "/data/CCBR_Pipeliner/db/PipeDB/snpEff_db/dbNSFP2.9.txt.gz",
"SNPEFF_CONFIG": "/usr/local/apps/snpEff/4.3t/snpEff.config",
# "FILTERSIFT": "(FILTER='PASS') & ( QUAL >= 20 )", ###maybe change to 30
# "FILTERSIFT": "( QUAL >= 20 )",
"SELECTDB": "SIFT_score,SIFT_pred,Polyphen2_HVAR_score,Polyphen2_HVAR_pred,LRT_score,LRT_pred,GERP++_RS,MutationAssessor_score,MutationAssessor_pred,1000Gp1_AF,1000Gp1_EUR_AF,ESP6500_EA_AF,ESP6500_AA_AF",
"SNPEFF_GENOME": "GRCh38.86",
"HAPMAP_DBNSFP": "/data/CCBR_Pipeliner/db/PipeDB/lib/snpEff_db/hapmap.bed",
"REGULOMEDB": "/data/CCBR_Pipeliner/db/PipeDB/lib/snpEff_db/RegulomeDB.bed",
"MUTECTCOSMIC": "/data/CCBR_Pipeliner/db/PipeDB/lib/COSMIC_82_hg38.vcf.gz",
"MUTECTSNP": "/fdb/GATK_resource_bundle/hg38bundle/dbsnp_138.hg38.vcf.gz",
"MUTECTGENOME": "/data/CCBR_Pipeliner/db/PipeDB/lib/GRCh38.d1.vd1.fa",
"MUTECTVARIANTS": "--dbsnp /fdb/GATK_resource_bundle/hg38bundle/dbsnp_138.hg38.vcf.gz --cosmic /data/CCBR_Pipeliner/db/PipeDB/lib/COSMIC_82_hg38.vcf.gz",
"VEPBUILD": "GRCh38",
"VEPSPECIES": "homo_sapiens",
"VEPFILTERVCF": "/data/CCBR_Pipeliner/db/PipeDB/lib/ExAC_nonTCGA.r1.sites.hg38.vep.vcf.gz",
"VEPGENOME": "/fdb/VEP/88/cache/GRCh38.fa",
"CANVASGENOME": "/data/CCBR_Pipeliner/db/PipeDB/lib/canvas_refs/GRCh38/WholeGenomeFasta",
"CANVASKMER": "/data/CCBR_Pipeliner/db/PipeDB/lib/canvas_refs/GRCh38/kmer.fa",
"CANVASFILTER": "/data/CCBR_Pipeliner/db/PipeDB/lib/canvas_refs/GRCh38/filter13.bed",
"CNVKITANNO": "/data/CCBR_Pipeliner/db/PipeDB/lib/hg38_refFlat.txt",
},
"genomeseq": {
"BWAGENOME": "/data/CCBR_Pipeliner/db/PipeDB/lib/GRCh38.d1.vd1.fa",
"PON": "/data/CCBR_Pipeliner/db/PipeDB/lib/1kGenomes_ExAC_0.001freq_PON.hg38.vcf.gz",
"GENOME": "/data/CCBR_Pipeliner/db/PipeDB/lib/GRCh38.d1.vd1.fa",
"CNVKITGENOME": "/data/CCBR_Pipeliner/db/PipeDB/lib/GRCh38.d1.vd1.fa",
"CNVKITREF": "/data/CCBR_Pipeliner/db/PipeDB/lib/GRCh38.d1.vd1_flatRef.cnn",
"CNVKITACCESS": "/data/CCBR_Pipeliner/db/PipeDB/lib/access-5k-mappable.grch38.bed",
"CNVKITANTITARGETS": "/data/CCBR_Pipeliner/db/PipeDB/lib/fake.antitargetcoverage.cnn",
"ADMIXTUREKEY": "/data/CCBR_Pipeliner/db/PipeDB/lib/1k_genomes_superpop_key.txt",
"ADMIXTUREREFS": "5",
"CNVKITANNO": "/data/CCBR_Pipeliner/db/PipeDB/lib/hg38_refFlat.txt",
"INDELSITES": "/fdb/GATK_resource_bundle/hg38bundle/Mills_and_1000G_gold_standard.indels.hg38.vcf.gz",
# "NOVOINDEX": "/data/CCBR_Pipeliner/db/PipeDB/lib/human_g1k_v37_iupac.nix",
# "REFFLAT": "/data/CCBR_Pipeliner/db/PipeDB/lib/reformatS04380219_qualimap.bed",
"KNOWNANCESTRY": "/data/CCBR_Pipeliner/db/PipeDB/lib/1k_genomes_phase3_autosomes.hg38.vcf.gz",
"ADMIXTUREKEY": "/data/CCBR_Pipeliner/db/PipeDB/lib/1k_genomes_superpop_key.txt",
"ADMIXTUREREFS": "5",
# "KNOWNVCF": "/data/CCBR_Pipeliner/db/PipeDB/lib/1k_genomes_compSet.vcf",
"KNOWNVCF2": "/fdb/GATK_resource_bundle/hg38bundle/1000G_phase1.snps.high_confidence.hg38.vcf.gz",
"SNPSITES": "/fdb/GATK_resource_bundle/hg38bundle/dbsnp_146.hg38.vcf.gz",
"KNOWNINDELS": "-known /fdb/GATK_resource_bundle/hg38bundle/Mills_and_1000G_gold_standard.indels.hg38.vcf.gz -known /data/CCBR_Pipeliner/db/PipeDB/lib/ALL.wgs.1000G_phase3.GRCh38.ncbi_remapper.20150424.shapeit2_indels.vcf.gz",
"KNOWNRECAL": "-knownSites /fdb/GATK_resource_bundle/hg38bundle/dbsnp_138.hg38.vcf.gz -knownSites /fdb/GATK_resource_bundle/hg38bundle/Mills_and_1000G_gold_standard.indels.hg38.vcf.gz -knownSites /data/CCBR_Pipeliner/db/PipeDB/lib/ALL.wgs.1000G_phase3.GRCh38.ncbi_remapper.20150424.shapeit2_indels.vcf.gz",
"THETASNPS": "/data/CCBR_Pipeliner/db/PipeDB/lib/hg38_theta_SNPfile.txt",
"INDELSITES2": "/data/CCBR_Pipeliner/db/PipeDB/lib/ALL.wgs.1000G_phase3.GRCh38.ncbi_remapper.20150424.shapeit2_indels.vcf.gz",
"ALVIEWGENOME": "hg38",
"CONPAIRMARKERSA": "/data/CCBR_Pipeliner/db/PipeDB/lib/hg38.autosomes.phase3_shapeit2_mvncall_integrated.20130502.SNV.genotype.sselect_v4_MAF_0.4_LD_0.8.txt",
"CONPAIRMARKERSB": "/data/CCBR_Pipeliner/db/PipeDB/lib/hg38.autosomes.phase3_shapeit2_mvncall_integrated.20130502.SNV.genotype.sselect_v4_MAF_0.4_LD_0.8.bed",
"EXONS": "/data/CCBR_Pipeliner/db/PipeDB/lib/hg38_exons.bed",
# "ANNDIR": "/data/CCBR_Pipeliner/db/PipeDB/AnnovarDB/",
"STRELKA_CONFIG": "/data/CCBR_Pipeliner/db/PipeDB/lib/strelka_demo_config.ini",
"DELLY_EXCLUSIONS": "/data/CCBR_Pipeliner/db/PipeDB/lib/delly.human.hg38.excl.tsv",
"FASTQ_SCREEN_CONFIG": "/data/CCBR_Pipeliner/db/PipeDB/lib/fastq_screen.conf",
"tg_GS_INDELS": "/fdb/GATK_resource_bundle/hg38bundle/Mills_and_1000G_gold_standard.indels.hg38.vcf.gz",
"tg_PHASE_INDELS": "/data/CCBR_Pipeliner/db/PipeDB/lib/ALL.wgs.1000G_phase3.GRCh38.ncbi_remapper.20150424.shapeit2_indels.vcf.gz",
"SNP138": "/fdb/GATK_resource_bundle/hg38bundle/dbsnp_138.hg38.vcf.gz",
"HAPMAP": "/fdb/GATK_resource_bundle/hg38bundle/hapmap_3.3.hg38.vcf.gz",
"B1K": "/fdb/GATK_resource_bundle/hg38bundle/1000G_phase1.snps.high_confidence.hg38.vcf.gz",
"OMNI": "/fdb/GATK_resource_bundle/hg38bundle/1000G_omni2.5.hg38.vcf.gz",
"adapter.file": "/data/CCBR_Pipeliner/db/PipeDB/dev/TruSeq_and_nextera_adapters.ngsqc.dat",
"fastqc.adapters": "/data/CCBR_Pipeliner/db/PipeDB/dev/fastqc.adapters",
"trimmomatic.adapters": "/data/CCBR_Pipeliner/db/PipeDB/dev/adapters2.fa",
"ORGANISM": "HUMAN",
"AVIASET": "hg38",
"ADAPTER1": "AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC",
"ADAPTER2": "AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT",
"nextera1": "CTGTCTCTTATACACATCTCCGAGCCCACGAGAC",
"nextera2": "CTGTCTCTTATACACATCTGACGCTGCCGACGA",
# "DB29": "/data/CCBR_Pipeliner/db/PipeDB/snpEff_db/dbNSFP2.9.txt.gz",
"SNPEFF_CONFIG": "/usr/local/apps/snpEff/4.3t/snpEff.config",
# "FILTERSIFT": "(FILTER='PASS') & ( QUAL >= 20 )", ###maybe change to 30
# "FILTERSIFT": "( QUAL >= 20 )",
"SELECTDB": "SIFT_score,SIFT_pred,Polyphen2_HVAR_score,Polyphen2_HVAR_pred,LRT_score,LRT_pred,GERP++_RS,MutationAssessor_score,MutationAssessor_pred,1000Gp1_AF,1000Gp1_EUR_AF,ESP6500_EA_AF,ESP6500_AA_AF",
"SNPEFF_GENOME": "GRCh38.86",
"HAPMAP_DBNSFP": "/data/CCBR_Pipeliner/db/PipeDB/lib/snpEff_db/hapmap.bed",
"REGULOMEDB": "/data/CCBR_Pipeliner/db/PipeDB/lib/snpEff_db/RegulomeDB.bed",
"MUTECTCOSMIC": "/data/CCBR_Pipeliner/db/PipeDB/lib/COSMIC_82_hg38.vcf.gz",
"MUTECTSNP": "/fdb/GATK_resource_bundle/hg38bundle/dbsnp_138.hg38.vcf.gz",
"MUTECTGENOME": "/data/CCBR_Pipeliner/db/PipeDB/lib/GRCh38.d1.vd1.fa",
"MUTECTVARIANTS": "--dbsnp /fdb/GATK_resource_bundle/hg38bundle/dbsnp_138.hg38.vcf.gz --cosmic /data/CCBR_Pipeliner/db/PipeDB/lib/COSMIC_82_hg38.vcf.gz",
"VEPBUILD": "GRCh38",
"VEPSPECIES": "homo_sapiens",
"VEPFILTERVCF": "/data/CCBR_Pipeliner/db/PipeDB/lib/ExAC_nonTCGA.r1.sites.hg38.vep.vcf.gz",
"VEPGENOME": "/fdb/VEP/88/cache/GRCh38.fa",
"CANVASGENOME": "/data/CCBR_Pipeliner/db/PipeDB/lib/canvas_refs/GRCh38/WholeGenomeFasta",
"CANVASKMER": "/data/CCBR_Pipeliner/db/PipeDB/lib/canvas_refs/GRCh38/kmer.fa",
"CANVASFILTER": "/data/CCBR_Pipeliner/db/PipeDB/lib/canvas_refs/GRCh38/filter13.bed",
"CNVKITANNO": "/data/CCBR_Pipeliner/db/PipeDB/lib/hg38_refFlat.txt",
},
"rnaseq": {
"GENOMEFILE": "/fdb/GENCODE/Gencode_human/release_26/GRCh38.primary_assembly.genome.fa",
"GTFFILE": "/fdb/GENCODE/Gencode_human/release_26/gencode.v26.annotation.gtf",
"ANNOTATE": "/data/CCBR_Pipeliner/db/PipeDB/dev/Hg38_genes_R26.txt",
"ANNOTATEISOFORMS": "/data/CCBR_Pipeliner/db/PipeDB/dev/Hg38_isoforms_R26.txt",
"REFFLAT": "/data/CCBR_Pipeliner/db/PipeDB/dev/refFlatHg38_R26.txt",
"BEDREF": "/data/CCBR_Pipeliner/db/PipeDB/lib/hg38.gencode.v26.bed",
"GENEINFO": "/data/CCBR_Pipeliner/db/PipeDB/dev/hg.v26.gencode.gtf.pre.bed",
"KARYOBEDS": "/data/CCBR_Pipeliner/db/PipeDB/dev/karyobeds/hg.v26/",
"RSEMREF": "/data/CCBR_Pipeliner/db/PipeDB/Rnaseq/rsem1.3.0/hg38_R26/human_gencode",
"STARDIR": "/fdb/STAR_indices/2.5.2b/GENCODE/Gencode_human/release_26/genes-",
"RRNALIST": "/data/CCBR_Pipeliner/db/PipeDB/dev/Hg38.rRNA.interval_list_R26",
"ADMIXTUREKEY": "/data/CCBR_Pipeliner/db/PipeDB/lib/1k_genomes_superpop_key.txt",
"ADMIXTUREREFS": "5",
"FASTQ_SCREEN_CONFIG": "/data/CCBR_Pipeliner/db/PipeDB/lib/fastq_screen.conf",
"FUSIONGTFFILE": "/fdb/GENCODE/Gencode_human/release_26/gencode.v26.annotation.gtf",
# "REFFLAT2": "/data/CCBR_Pipeliner/db/PipeDB/dev/refFlatHg38_R26.txt",
# "SALMONREF": "/data/CCBR_Pipeliner/db/PipeDB/Rnaseq/rsem1.3.0/hg38_R26/human_gencode.transcripts.fa",
# "FASTAWITHADAPTERSETC": "/data/CCBR_Pipeliner/dev/RNA-Seq-pipeline/ver2/TruSeq_and_nextera_adapters_new.fa",
"FASTAWITHADAPTERSETC": "/data/CCBR_Pipeliner/db/PipeDB/dev/TruSeq_and_nextera_adapters_new.fa",
"STARREF": "/fdb/STAR_indices/2.5.2b/GENCODE/Gencode_human/release_26/genes-",
# "RRNALIST2": "/data/CCBR_Pipeliner/db/PipeDB/dev/Hg38.rRNA.interval_list_R26",
"STARFUSIONLIB": "/data/CCBR_Pipeliner/db/PipeDB/lib/GRCh38_gencode_v24_CTAT_lib_Mar292017_prebuilt",
"FUSCATCHDAT": "/usr/local/apps/fusioncatcher/1.00/fusioncatcher/data/human_v90",
"FUSCATCHCONFIG": "/data/CCBR_Pipeliner/db/PipeDB/lib/hg19_hg38_configuration.cfg",
"GENOME": "/fdb/GENCODE/Gencode_human/release_26/GRCh38.primary_assembly.genome.fa",
# "INDELSITES": "/fdb/GATK_resource_bundle/hg38bundle/Mills_and_1000G_gold_standard.indels.hg38.vcf.gz",
"KNOWNANCESTRY": "/data/CCBR_Pipeliner/db/PipeDB/lib/1k_genomes_phase3_autosomes.hg38.vcf.gz",
"KNOWNVCF": "/data/CCBR_Pipeliner/db/PipeDB/lib/1k_genomes_compSet.vcf",
"KNOWNVCF2": "/fdb/GATK_resource_bundle/hg38bundle/1000G_phase1.snps.high_confidence.hg38.vcf.gz",
"SNPSITES": "/fdb/GATK_resource_bundle/hg38bundle/dbsnp_146.hg38.vcf.gz",
"KNOWNINDELS": "-known /fdb/GATK_resource_bundle/hg38bundle/Mills_and_1000G_gold_standard.indels.hg38.vcf.gz -known /data/CCBR_Pipeliner/db/PipeDB/lib/ALL.wgs.1000G_phase3.GRCh38.ncbi_remapper.20150424.shapeit2_indels.vcf.gz",
"KNOWNRECAL": "-knownSites /fdb/GATK_resource_bundle/hg38bundle/dbsnp_138.hg38.vcf.gz -knownSites /fdb/GATK_resource_bundle/hg38bundle/Mills_and_1000G_gold_standard.indels.hg38.vcf.gz -knownSites /data/CCBR_Pipeliner/db/PipeDB/lib/ALL.wgs.1000G_phase3.GRCh38.ncbi_remapper.20150424.shapeit2_indels.vcf.gz",
# "THETASNPS": "/data/CCBR_Pipeliner/db/PipeDB/lib/hg38_theta_SNPfile.txt",
"INDELSITES2": "/data/CCBR_Pipeliner/db/PipeDB/lib/ALL.wgs.1000G_phase3.GRCh38.ncbi_remapper.20150424.shapeit2_indels.vcf.gz",
"ALVIEWGENOME": "hg38",
"ONCOFUSEBUILD": "hg38",
"EXONS": "/data/CCBR_Pipeliner/db/PipeDB/lib/hg38_exons.bed",
# "ANNDIR": "/data/CCBR_Pipeliner/db/PipeDB/AnnovarDB/",
# "tg_GS_INDELS": "/fdb/GATK_resource_bundle/hg38bundle/Mills_and_1000G_gold_standard.indels.hg38.vcf.gz",
# "tg_PHASE_INDELS": "/data/CCBR_Pipeliner/db/PipeDB/lib/ALL.wgs.1000G_phase3.GRCh38.ncbi_remapper.20150424.shapeit2_indels.vcf.gz",
# "SNP138": "/fdb/GATK_resource_bundle/hg38bundle/dbsnp_138.hg38.vcf.gz",
# "HAPMAP": "/fdb/GATK_resource_bundle/hg38bundle/hapmap_3.3.hg38.vcf.gz",
# "B1K": "/fdb/GATK_resource_bundle/hg38bundle/1000G_phase1.snps.high_confidence.hg38.vcf.gz",
# "OMNI": "/fdb/GATK_resource_bundle/hg38bundle/1000G_omni2.5.hg38.vcf.gz",
"adapter.file": "/data/CCBR_Pipeliner/db/PipeDB/dev/TruSeq_and_nextera_adapters.ngsqc.dat",
"fastqc.adapters": "/data/CCBR_Pipeliner/db/PipeDB/dev/fastqc.adapters",
"trimmomatic.adapters": "/data/CCBR_Pipeliner/db/PipeDB/dev/adapters2.fa",
"ORGANISM": "HUMAN",
"AVIASET": "hg38",
# "ADAPTER1": "AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC",
# "ADAPTER2": "AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT",
# "nextera1": "CTGTCTCTTATACACATCTCCGAGCCCACGAGAC",
# "nextera2": "CTGTCTCTTATACACATCTGACGCTGCCGACGA",
# "DB29": "/data/CCBR_Pipeliner/db/PipeDB/snpEff_db/dbNSFP2.9.txt.gz",
# "SELECTDB": "SIFT_score,SIFT_pred,Polyphen2_HVAR_score,Polyphen2_HVAR_pred,LRT_score,LRT_pred,GERP++_RS,MutationAssessor_score,MutationAssessor_pred,1000Gp1_AF,1000Gp1_EUR_AF,ESP6500_EA_AF,ESP6500_AA_AF",
"SNPEFF_GENOME": "GRCh38.86",
"SNPEFF_CONFIG": "/usr/local/apps/snpEff/4.3t/snpEff.config",
# "HAPMAP_DBNSFP": "/data/CCBR_Pipeliner/db/PipeDB/lib/snpEff_db/hapmap.bed",
# "REGULOMEDB": "/data/CCBR_Pipeliner/db/PipeDB/lib/snpEff_db/RegulomeDB.bed",
},
"rnaseqvargerm": {
"GENOMEFILE": "/fdb/GENCODE/Gencode_human/release_19/GRCh37.p13.genome.fa",
"GTFFILE": "/data/CCBR_Pipeliner/db/PipeDB/lib/GENCODE_GRCh37_ref_annot.gtf",
"ANNOTATE": "/data/CCBR_Pipeliner/db/PipeDB/dev/Hg19_genes.txt",
"BEDREF": "/data/CCBR_Pipeliner/db/PipeDB/lib/hg19_GENCODE_GENE_V19_comprehensive.bed",
"RSEMREF": "/data/CCBR_Pipeliner/db/PipeDB/Rnaseq/human_gencode",
"SALMONREF": "/data/CCBR_Pipeliner/db/PipeDB/Rnaseq/human_gencode.transcripts.fa",
"FASTAWITHADAPTERSETC": "/data/CCBR_Pipeliner/db/PipeDB/dev/TruSeq_and_nextera_adapters_new.fa",
"STARDIR": "/fdb/STAR_2.4.2a/GENCODE/Gencode_human/release_19/genes-",
"STARREF": "/data/CCBR_Pipeliner/db/PipeDB/lib/Star_refs/hs37d5/genes-",
"RRNALIST": "/data/CCBR_Pipeliner/db/PipeDB/dev/Hg19.rRNA.interval_list_v3",
# "BWAGENOME": "/data/CCBR_Pipeliner/db/PipeDB/lib/hs37d5.fa",
"CHROMS": ["1","2","3","4","5","6","7","8","9","10","11","12","13","14","15","16","17","18","19","20","21","22","X","Y","MT"],
# "GENOME": "/data/CCBR_Pipeliner/db/PipeDB/lib/hs37d5.fa",
"CNVKITGENOME": "/data/CCBR_Pipeliner/db/PipeDB/lib/hs37d5.fa",
"CNVKITACCESS": "/data/CCBR_Pipeliner/db/PipeDB/lib/access-5k-mappable.grch37.bed",
"ADMIXTUREKEY": "/data/CCBR_Pipeliner/db/PipeDB/lib/1k_genomes_superpop_key.txt",
"ADMIXTUREREFS": "5",
"INDELSITES": "/fdb/GATK_resource_bundle/b37/Mills_and_1000G_gold_standard.indels.b37.vcf",
"NOVOINDEX": "/data/CCBR_Pipeliner/db/PipeDB/lib/human_g1k_v37_iupac.nix",
"REFFLAT": "/data/CCBR_Pipeliner/db/PipeDB/dev/refFlatHg19.txt",
"KNOWNANCESTRY": "/data/CCBR_Pipeliner/db/PipeDB/lib/1k_genomes_phase3_autosomes.vcf.gz",
"KNOWNVCF": "/data/CCBR_Pipeliner/db/PipeDB/lib/1k_genomes_compSet.vcf",
"KNOWNVCF2": "/fdb/GATK_resource_bundle/b37-2.8/1000G_phase3_v4_20130502.sites.vcf.gz",
"SNPSITES": "/fdb/GATK_resource_bundle/b37/dbsnp_138.b37.vcf",
"KNOWNINDELS": "-known /fdb/GATK_resource_bundle/b37/Mills_and_1000G_gold_standard.indels.b37.vcf -known /fdb/GATK_resource_bundle/b37/1000G_phase1.indels.b37.vcf",
"KNOWNRECAL": "-knownSites /fdb/GATK_resource_bundle/b37/dbsnp_138.b37.vcf -knownSites /fdb/GATK_resource_bundle/b37/Mills_and_1000G_gold_standard.indels.b37.vcf -knownSites /fdb/GATK_resource_bundle/b37/1000G_phase1.indels.b37.vcf",
"THETASNPS": "/data/CCBR_Pipeliner/db/PipeDB/lib/hg19_theta_SNPfile.txt",
"INDELSITES2": "/fdb/GATK_resource_bundle/b37/1000G_phase1.indels.b37.vcf",
"ALVIEWGENOME": "hg19",
"CONPAIRMARKERS": "/data/CCBR_Pipeliner/db/PipeDB/lib/GRCh37.autosomes.phase3_shapeit2_mvncall_integrated.20130502.SNV.genotype.sselect_v4_MAF_0.4_LD_0.8.txt",
"EXONS": "/data/CCBR_Pipeliner/db/PipeDB/lib/hg19.exons.bed",
"ANNDIR": "/data/CCBR_Pipeliner/db/PipeDB/AnnovarDB/",
"STRELKA_CONFIG": "/data/CCBR_Pipeliner/db/PipeDB/lib/strelka_demo_config.ini",
"CNVKIT_TARGETS": "/data/CCBR_Pipeliner/db/PipeDB/lib/human_SSv5_cnvkit_targets.bed",
"CNVKIT_ANTITARGETS": "/data/CCBR_Pipeliner/db/PipeDB/lib/human_SSv5_cnvkit_antitargets.bed",
"CNVKITACCESS": "/data/CCBR_Pipeliner/db/PipeDB/lib/access-5k-mappable.grch37.bed",
"DELLY_EXCLUSIONS": "/data/CCBR_Pipeliner/db/PipeDB/lib/delly.human.hg19.excl.tsv",
"FASTQ_SCREEN_CONFIG": "/data/CCBR_Pipeliner/db/PipeDB/lib/fastq_screen.conf",
"tg_GS_INDELS": "/fdb/GATK_resource_bundle/hg19-2.8/Mills_and_1000G_gold_standard.indels.hg19.vcf.gz",
"tg_PHASE_INDELS": "/fdb/GATK_resource_bundle/hg19-2.8/1000G_phase1.indels.hg19.vcf.gz",
"SNP138": "/fdb/GATK_resource_bundle/hg19-2.8/dbsnp_138.hg19.vcf.gz",
"HAPMAP": "/fdb/GATK_resource_bundle/hg19-2.8/hapmap_3.3.hg19.vcf.gz",
"B1K": "/fdb/GATK_resource_bundle/hg19-2.8/1000G_phase1.snps.high_confidence.hg19.vcf.gz",
"OMNI": "/fdb/GATK_resource_bundle/hg19-2.8/1000G_omni2.5.hg19.vcf.gz",
"adapter.file": "/data/CCBR_Pipeliner/db/PipeDB/dev/TruSeq_and_nextera_adapters.ngsqc.dat",
"fastqc.adapters": "/data/CCBR_Pipeliner/db/PipeDB/dev/fastqc.adapters",
"trimmomatic.adapters": "/data/CCBR_Pipeliner/db/PipeDB/dev/adapters2.fa",
"ORGANISM": "HUMAN",
"AVIASET": "hg19",
"ADAPTER1": "AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC",
"ADAPTER2": "AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT",
"nextera1": "CTGTCTCTTATACACATCTCCGAGCCCACGAGAC",
"nextera2": "CTGTCTCTTATACACATCTGACGCTGCCGACGA",
"gencodeGtf":"gencode.vM4.all.gtf",
"genomeRnaseq": "GRCm38.p3.genome.fa",
"genomeDir": "/data/CCBR_Pipeliner/db/PipeDB/lib/genomes",
"gtfDir": "/data/CCBR_Pipeliner/db/PipeDB/lib/gtf",
"genomeDir2": "/data/CCBR_Pipeliner/db/PipeDB/lib/genomes/2pass",
"gtfERCC": "gencode.vM4.all_ERCC.gtf",
"genomeRnaseqErcc": "GRCm38.p3.ERCC.genome.fa",
"DB29": "/data/CCBR_Pipeliner/db/PipeDB/snpEff_db/dbNSFP2.9.txt.gz",
"SNPEFF_CONFIG": "/usr/local/apps/snpEff/4.3t/snpEff.config",
"SELECTDB": "SIFT_score,SIFT_pred,Polyphen2_HVAR_score,Polyphen2_HVAR_pred,LRT_score,LRT_pred,GERP++_RS,MutationAssessor_score,MutationAssessor_pred,1000Gp1_AF,1000Gp1_EUR_AF,ESP6500_EA_AF,ESP6500_AA_AF",
"SNPEFF_GENOME": "GRCh37.75",
"HAPMAP_DBNSFP": "/data/CCBR_Pipeliner/db/PipeDB/lib/snpEff_db/hapmap.bed",
"REGULOMEDB": "/data/CCBR_Pipeliner/db/PipeDB/lib/snpEff_db/RegulomeDB.bed",
"MUTECTCOSMIC": "/data/CCBR_Pipeliner/db/PipeDB/lib/COSMIC_82_hg38.vcf.gz",
"MUTECTSNP": "/fdb/muTect/dbsnp_137.b37.vcf",
"MUTECTGENOME": "/fdb/muTect/human_g1k_v37.fasta",
"MUTECTVARIANTS": "--dbsnp /fdb/muTect/dbsnp_137.b37.vcf --cosmic /data/CCBR_Pipeliner/db/PipeDB/lib/COSMIC_82_hg38.vcf.gz"
},
"mirseq": {
"run_info":{
"TOOL": "miRNA",
"VERSION": "1.1",
"PI": "NA",
"FLOWCELL": "external",
"GENOME_BUILD": "hg38",
"MIRBASE_VERSION": "21",
"EMAIL": "david.wheeler3@nih.gov",
# "SAMPLENAMES": "dA549-KD-a-1_S4_R1_001:dA549-NCTR-a-1_S1_R1_001:dA549-KO-a-2_S5_R1_001:dA549-NCTR-a-2_S3_R1_001:dA549-KD-b-1_S8_R1_001:dA549-NCTR-b-1_S6_R1_001:dA549-KD-b-2_S2_R1_001:dA549-NCTR-b-2-2_S2_R1_001:dH460-KOa-1_S3_R1_001:dH460-NCTR-a-1_S1_R1_001:dH460-KOa-2_S4_R1_001:dH460-NCTR-a-2_S2_R1_001:dH460-KO-b-1_S6_R1_001:dH460-NCTR-b-1_S5_R1_001:dH460-KO-b-2_S8_R1_001:dH460-NCTR-b-2-2_S1_R1_001",
# "LANEINDEX": "-:-:-:-",
"TRIM_ADAPTER": "YES",
"CALL_SNVS": "YES",
"DIFF_EXPRESSION": "YES",
"DIFF_EXPRESSION_ANALYSES": "mir_knockdown",
# "INPUT_DIR": "/",
# "OUTPUT_DIR": "out",
"TOOL_INFO": "tool_info",
"SAMPLE_INFO": "sample_info",
# "DELIVERY_FOLDER": "/scratch/dwheeler/test5/out",
# "USE_SGE": "0",
# "USE_PORTAL": "0",
# "PORTAL_PROJECT_NAME": "NA"
},
"reference_files": {
"BOWTIE_REF": "/data/CCBR_Pipeliner/db/PipeDB/miRseq/References/genome",
"GENCODE_GTF": "/fdb/GENCODE/GRCh38/21/GTF/gencode.v21.annotation.gtf",
"MIRBASE_GFF": "/data/CCBR_Pipeliner/db/PipeDB/miRseq/References/hsa.gff3",
"MIRBASE_HAIRPIN": "/data/CCBR_Pipeliner/db/PipeDB/miRseq/References/hairpin.fa",
"MIRBASE_MATURE": "/data/CCBR_Pipeliner/db/PipeDB/miRseq/References/mature.fa",
# For miRspring which uses its own set of files
"MIRBASE_FILES": "/data/CCBR_Pipeliner/db/PipeDB/miRseq/References",
# "MIRBASE_GFF": "/data/dwheeler/miRspring/miRbase_Files/hsa.gff2",
# "MIRBASE_HAIRPIN": "/data/dwheeler/miRspring/miRbase_Files/hsa.nt35.fa",
# "MIRBASE_MATURE": "/data/dwheeler/miRspring/miRbase_Files/mature.fa",
# "MIRBASE_FILES": "/data/dwheeler/miRspring/miRbase_Files/",
"REF_GENOME": "/data/CCBR_Pipeliner/db/PipeDB/miRseq/References/genome.fa",
"REF_GENOME_IUPAC": "/data/CCBR_Pipeliner/db/PipeDB/miRseq/References/genome-iupac.fa",
"TARGET_DATA": "/data/CCBR_Pipeliner/db/PipeDB/miRseq/References",
},
},
"chipseq":{},
}
}