GPF Study Configuration
id- ID of the study. This is a required field.name- display name of the study. If thenameis not specified, theidwill be used as the display name.enabled- whether the study is enabled.description_file- path to the study description file.study_phenotype- study phenotype.has_denovo- whether the study has de novo variants.has_transmitted- whether the study has transmitted variants.has_cnv- whether the study has CNV variants.has_complex- whether the study has complex variants.has_tandem_repeat- whether the study has tandem repeat variants.has_zygosity- whether the study has zygosity information.phenotype_data- phenotype data associated with the study.phenotype_browser- whether the phenotype browser is enabled.phenotype_tool- whether the phenotype tool is enabled.person_set_collections- section to define person set collections associated with the study.genotype_storage- section to define genotype storage configuration for the study.genotype browser- section to define genotype browser configuration for the study.common_report- section to define common report configuration for the study.denovo_gene_sets- section to define de novo gene sets configuration for the study.enrichment- section to define enrichment configuration for the study.gene_browser- section to define gene browser configuration for the study.
1id: example_study
2phenotype_browser: false
3phenotype_tool: false
4study_type:
5- WE
6study_phenotype: autism
7has_transmitted: false
8has_denovo: true
9has_complex: false
10has_cnv: false
11
12person_set_collections:
13 selected_person_set_collections:
14 - phenotype
15 phenotype:
16 id: phenotype
17 name: Phenotype
18 sources:
19 - from: pedigree
20 source: status
21 domain:
22 - id: autism
23 name: autism
24 values:
25 - affected
26 color: '#ff2121'
27 - id: unaffected
28 name: unaffected
29 values:
30 - unaffected
31 color: '#ffffff'
32 default:
33 id: unspecified
34 name: unspecified
35 color: '#aaaaaa'
36
37genotype_browser:
38 enabled: true
39
40 has_present_in_child: true
41 has_present_in_parent: true
42 has_pedigree_selector: true
43
44 variant_types:
45 - sub
46 - ins
47 - del
48 - complex
49 columns:
50 genotype:
51 pedigree:
52 name: pedigree
53 source: pedigree
54 worst_effect:
55 name: worst effect
56 source: worst_effect
57 genes:
58 name: genes
59 source: genes
60 lgd_rank:
61 name: LGD rank
62 source: LGD_rank
63 format: '%%d'
64 rvis_rank:
65 name: RVIS rank
66 source: RVIS_rank
67 format: '%%d'
68 pli_rank:
69 name: pLI rank
70 source: pLI_rank
71 format: '%%d'
72 family_id:
73 name: family id
74 source: family
75 study:
76 name: study
77 source: study_name
78 family_person_ids:
79 name: family person ids
80 source: family_person_ids
81 location:
82 name: location
83 source: location
84 variant:
85 name: variant
86 source: variant
87 chrom:
88 name: CHROM
89 source: chrom
90 position:
91 name: POS
92 source: position
93 reference:
94 name: REF
95 source: reference
96 alternative:
97 name: ALT
98 source: alternative
99 carrier_person_ids:
100 name: carrier person ids
101 source: carrier_person_ids
102 carrier_person_attributes:
103 name: carrier person attributes
104 source: carrier_person_attributes
105 family_person_attributes:
106 name: family person attributes
107 source: family_person_attributes
108 family_phenotypes:
109 name: family phenotypes
110 source: family_phenotypes
111 carrier_phenotypes:
112 name: carrier phenotypes
113 source: carrier_phenotypes
114 inheritance:
115 name: inheritance type
116 source: inheritance_type
117 study_phenotype:
118 name: study phenotype
119 source: study_phenotype
120 best:
121 name: family best state
122 source: best_st
123 family_genotype:
124 name: family genotype
125 source: genotype
126 family_structure:
127 name: family structure
128 source: family_structure
129 geneeffect:
130 name: all effects
131 source: effects
132 effectdetails:
133 name: effect details
134 source: effect_details
135 alt_alleles:
136 name: alt alleles
137 source: af_allele_count
138 par_called:
139 name: parents called
140 source: af_parents_called_count
141 allele_freq:
142 name: allele frequency
143 source: af_allele_freq
144 seen_as_denovo:
145 name: seen_as_denovo
146 source: seen_as_denovo
147 seen_in_affected:
148 name: seen_in_affected
149 source: seen_in_affected
150 seen_in_unaffected:
151 name: seen_in_unaffected
152 source: seen_in_unaffected
153 phylop_phylop100way:
154 name: 100way
155 source: phylop100way
156 format: '%%.3f'
157 phylop_phylop30way:
158 name: 30way
159 source: phylop30way
160 format: '%%.3f'
161 phylop_phylop20way:
162 name: 20way
163 source: phylop20way
164 format: '%%.3f'
165 phastcons_phastcons100way:
166 name: 100way
167 source: phastcons100way
168 format: '%%.3f'
169 phastcons_phastcons30way:
170 name: 30way
171 source: phastcons30way
172 format: '%%.3f'
173 phastcons_phastcons20way:
174 name: 20way
175 source: phastcons20way
176 format: '%%.3f'
177 fitcons_fitcons2_e073:
178 name: Prefrontal Cortex
179 source: fitcons2_e073
180 format: '%%.3f'
181 fitcons_fitcons2_e081:
182 name: ' Male Fetal'
183 source: fitcons2_e081
184 format: '%%.3f'
185 fitcons_fitcons2_e082:
186 name: Female Fetal
187 source: fitcons2_e082
188 format: '%%.3f'
189 freq_ssc:
190 name: SSC
191 source: ssc_freq
192 format: '%%.3f'
193 freq_exome_gnomad:
194 name: exome gnomAD
195 source: exome_gnomad_v2_1_1_af_percent
196 format: '%%.3f'
197 freq_genome_gnomad:
198 name: genome gnomAD
199 source: genome_gnomad_v3_af_percent
200 format: '%%.3f'
201 cadd_raw:
202 name: CADD raw
203 source: cadd_raw
204 format: '%%.3f'
205 cadd_phred:
206 name: CADD phred
207 source: cadd_phred
208 format: '%%.3f'
209 mpc:
210 name: MPC
211 source: mpc
212 format: '%%.3f'
213 linsight:
214 name: Linsight
215 source: linsight
216 format: '%%.3f'
217 genome_gnomad_v2_1_1_ac:
218 name: genome_gnomad_v2_1_1_ac
219 source: genome_gnomad_v2_1_1_ac
220 format: '%%d'
221 genome_gnomad_v2_1_1_an:
222 name: genome_gnomad_v2_1_1_an
223 source: genome_gnomad_v2_1_1_an
224 format: '%%d'
225 genome_gnomad_v2_1_1_controls_ac:
226 name: genome_gnomad_v2_1_1_controls_ac
227 source: genome_gnomad_v2_1_1_controls_ac
228 format: '%%d'
229 genome_gnomad_v2_1_1_controls_an:
230 name: genome_gnomad_v2_1_1_controls_an
231 source: genome_gnomad_v2_1_1_controls_an
232 format: '%%d'
233 genome_gnomad_v2_1_1_non_neuro_ac:
234 name: genome_gnomad_v2_1_1_non_neuro_ac
235 source: genome_gnomad_v2_1_1_non_neuro_ac
236 format: '%%d'
237 genome_gnomad_v2_1_1_non_neuro_an:
238 name: genome_gnomad_v2_1_1_non_neuro_an
239 source: genome_gnomad_v2_1_1_non_neuro_an
240 format: '%%d'
241 genome_gnomad_v2_1_1_af_percent:
242 name: genome_gnomad_v2_1_1_af_percent
243 source: genome_gnomad_v2_1_1_af_percent
244 format: '%%.3f'
245 genome_gnomad_v2_1_1_controls_af_percent:
246 name: genome_gnomad_v2_1_1_controls_af_percent
247 source: genome_gnomad_v2_1_1_controls_af_percent
248 format: '%%.3f'
249 genome_gnomad_v2_1_1_non_neuro_af_percent:
250 name: genome_gnomad_v2_1_1_non_neuro_af_percent
251 source: genome_gnomad_v2_1_1_non_neuro_af_percent
252 format: '%%.3f'
253 exome_gnomad_v2_1_1_ac:
254 name: exome_gnomad_v2_1_1_ac
255 source: exome_gnomad_v2_1_1_ac
256 format: '%%d'
257 exome_gnomad_v2_1_1_an:
258 name: exome_gnomad_v2_1_1_an
259 source: exome_gnomad_v2_1_1_an
260 exome_gnomad_v2_1_1_controls_ac:
261 name: exome_gnomad_v2_1_1_controls_ac
262 source: exome_gnomad_v2_1_1_controls_ac
263 format: '%%d'
264 exome_gnomad_v2_1_1_controls_an:
265 name: exome_gnomad_v2_1_1_controls_an
266 source: exome_gnomad_v2_1_1_controls_an
267 format: '%%d'
268 exome_gnomad_v2_1_1_non_neuro_ac:
269 name: exome_gnomad_v2_1_1_non_neuro_ac
270 source: exome_gnomad_v2_1_1_non_neuro_ac
271 format: '%%d'
272 exome_gnomad_v2_1_1_non_neuro_an:
273 name: exome_gnomad_v2_1_1_non_neuro_an
274 source: exome_gnomad_v2_1_1_non_neuro_an
275 format: '%%d'
276 exome_gnomad_v2_1_1_af_percent:
277 name: exome_gnomad_v2_1_1_af_percent
278 source: exome_gnomad_v2_1_1_af_percent
279 format: '%%.3f'
280 exome_gnomad_v2_1_1_controls_af_percent:
281 name: exome_gnomad_v2_1_1_controls_af_percent
282 source: exome_gnomad_v2_1_1_controls_af_percent
283 format: '%%.3f'
284 exome_gnomad_v2_1_1_non_neuro_af_percent:
285 name: exome_gnomad_v2_1_1_non_neuro_af_percent
286 source: exome_gnomad_v2_1_1_non_neuro_af_percent
287 format: '%%.3f'
288 genome_gnomad_v3_ac:
289 name: genome_gnomad_v3_ac
290 source: genome_gnomad_v3_ac
291 format: '%%d'
292 genome_gnomad_v3_an:
293 name: genome_gnomad_v3_an
294 source: genome_gnomad_v3_an
295 format: '%%d'
296 genome_gnomad_v3_af_percent:
297 name: genome_gnomad_v3_af_percent
298 source: genome_gnomad_v3_af_percent
299 format: '%%.3f'
300 phylop100way:
301 name: phyloP100way
302 source: phylop100way
303 format: '%%.3f'
304 phylop30way:
305 name: phyloP30way
306 source: phylop30way
307 format: '%%.3f'
308 phylop20way:
309 name: phyloP20way
310 source: phylop20way
311 format: '%%.3f'
312 phylop7way:
313 name: phyloP7way
314 source: phylop7way
315 format: '%%.3f'
316 phastcons100way:
317 name: phastCons100way
318 source: phastcons100way
319 format: '%%.3f'
320 phastcons30way:
321 name: phastCons30way
322 source: phastcons30way
323 format: '%%.3f'
324 phastcons20way:
325 name: phastCons20way
326 source: phastcons20way
327 format: '%%.3f'
328 phastcons7way:
329 name: phastCons7way
330 source: phastcons7way
331 format: '%%.3f'
332 fitcons_i6_merged:
333 name: FitCons i6 merged
334 source: fitcons_i6_merged
335 format: '%%.3f'
336 fitcons2_e067:
337 name: FitCons2 Brain Angular Gyrus
338 source: fitcons2_e067
339 format: '%%.3f'
340 fitcons2_e068:
341 name: FitCons2 Brain Anterior Caudate
342 source: fitcons2_e068
343 format: '%%.3f'
344 fitcons2_e069:
345 name: FitCons2 Brain Cingulate Gyrus
346 source: fitcons2_e069
347 format: '%%.3f'
348 fitcons2_e070:
349 name: FitCons2 Brain Germinal Matrix
350 source: fitcons2_e070
351 format: '%%.3f'
352 fitcons2_e071:
353 name: FitCons2 Brain Hippocampus Middle
354 source: fitcons2_e071
355 format: '%%.3f'
356 fitcons2_e072:
357 name: FitCons2 Brain Inferior Temporal Lobe
358 source: fitcons2_e072
359 format: '%%.3f'
360 fitcons2_e073:
361 name: FitCons2 Brain Dorsolateral Prefrontal Cortex
362 source: fitcons2_e073
363 format: '%%.3f'
364 fitcons2_e074:
365 name: FitCons2 Brain Substantia Nigra
366 source: fitcons2_e074
367 format: '%%.3f'
368 fitcons2_e081:
369 name: FitCons2 Fetal Brain Male
370 source: fitcons2_e081
371 format: '%%.3f'
372 fitcons2_e082:
373 name: FitCons2 Fetal Brain Female
374 source: fitcons2_e082
375 format: '%%.3f'
376
377 column_groups:
378 genotype:
379 name: genotype
380 columns:
381 - pedigree
382 - carrier_person_attributes
383 - family_person_attributes
384 effect:
385 name: effect
386 columns:
387 - worst_effect
388 - genes
389 gene_scores:
390 name: vulnerability/intolerance
391 columns:
392 - lgd_rank
393 - rvis_rank
394 - pli_rank
395 family:
396 name: family
397 columns:
398 - family_id
399 - study
400 variant:
401 name: variant
402 columns:
403 - location
404 - variant
405 variant_extra:
406 name: variant
407 columns:
408 - chrom
409 - position
410 - reference
411 - alternative
412 carriers:
413 name: carriers
414 columns:
415 - carrier_person_ids
416 - carrier_person_attributes
417 phenotypes:
418 name: phenotypes
419 columns:
420 - family_phenotypes
421 - carrier_phenotypes
422 mpc_cadd:
423 name: MPC and CADD
424 columns:
425 - mpc
426 - cadd_raw
427 - cadd_phred
428 phylop:
429 name: phyloP
430 columns:
431 - phylop_phylop100way
432 - phylop_phylop30way
433 - phylop_phylop20way
434 phastcons:
435 name: phastCons
436 columns:
437 - phastcons_phastcons100way
438 - phastcons_phastcons30way
439 - phastcons_phastcons20way
440 fitcons:
441 name: FitCons Brain
442 columns:
443 - fitcons_fitcons2_e073
444 - fitcons_fitcons2_e081
445 - fitcons_fitcons2_e082
446 freq:
447 name: Frequency
448 columns:
449 - freq_ssc
450 - freq_exome_gnomad
451 - freq_genome_gnomad
452
453 preview_columns:
454 - family
455 - variant
456 - genotype
457 - effect
458 - gene_scores
459 - phylop
460 - phastcons
461 - mpc_cadd
462 - fitcons
463 - freq
464 download_columns:
465 - family
466 - study_phenotype
467 - variant
468 - variant_extra
469 - family_person_ids
470 - family_structure
471 - best
472 - family_genotype
473 - carriers
474 - inheritance
475 - phenotypes
476 - par_called
477 - allele_freq
478 - effect
479 - geneeffect
480 - effectdetails
481 - gene_scores
482 - phylop100way
483 - phylop30way
484 - phylop20way
485 - phylop7way
486 - phastcons100way
487 - phastcons30way
488 - phastcons20way
489 - phastcons7way
490 - cadd_raw
491 - cadd_phred
492 - mpc
493 - linsight
494 - fitcons_i6_merged
495 - fitcons2_e067
496 - fitcons2_e068
497 - fitcons2_e069
498 - fitcons2_e070
499 - fitcons2_e071
500 - fitcons2_e072
501 - fitcons2_e073
502 - fitcons2_e074
503 - fitcons2_e081
504 - fitcons2_e082
505 - genome_gnomad_v2_1_1_ac
506 - genome_gnomad_v2_1_1_an
507 - genome_gnomad_v2_1_1_controls_ac
508 - genome_gnomad_v2_1_1_controls_an
509 - genome_gnomad_v2_1_1_non_neuro_ac
510 - genome_gnomad_v2_1_1_non_neuro_an
511 - genome_gnomad_v2_1_1_af_percent
512 - genome_gnomad_v2_1_1_controls_af_percent
513 - genome_gnomad_v2_1_1_non_neuro_af_percent
514 - exome_gnomad_v2_1_1_ac
515 - exome_gnomad_v2_1_1_an
516 - exome_gnomad_v2_1_1_controls_ac
517 - exome_gnomad_v2_1_1_controls_an
518 - exome_gnomad_v2_1_1_non_neuro_ac
519 - exome_gnomad_v2_1_1_non_neuro_an
520 - exome_gnomad_v2_1_1_af_percent
521 - exome_gnomad_v2_1_1_controls_af_percent
522 - exome_gnomad_v2_1_1_non_neuro_af_percent
523 - genome_gnomad_v3_ac
524 - genome_gnomad_v3_an
525 - genome_gnomad_v3_af_percent
526
527common_report:
528 enabled: true
529 effect_groups:
530 - LGDs
531 - nonsynonymous
532 - UTRs
533 - CNV
534 effect_types:
535 - Nonsense
536 - Frame-shift
537 - Splice-site
538 - Missense
539 - No-frame-shift
540 - noStart
541 - noEnd
542 - Synonymous
543 - Non coding
544 - Intron
545 - Intergenic
546 - 3'-UTR
547 - 5'-UTR
548
549denovo_gene_sets:
550 enabled: true
551 selected_person_set_collections:
552 - phenotype
553 standard_criterias:
554 effect_types:
555 segments:
556 LGDs: LGDs
557 Missense: missense
558 Synonymous: synonymous
559 sexes:
560 segments:
561 Female: F
562 Male: M
563 Unspecified: U
564 recurrency_criteria:
565 segments:
566 Single:
567 start: 1
568 end: 2
569 Triple:
570 start: 3
571 end: -1
572 Recurrent:
573 start: 2
574 end: -1
575 gene_sets_names:
576 - LGDs
577 - LGDs.Male
578 - LGDs.Female
579 - LGDs.Recurrent
580 - LGDs.Triple
581 - Missense
582 - Missense.Male
583 - Missense.Female
584 - Missense.Recurrent
585 - Missense.Triple
586 - Synonymous
587 - Synonymous.Male
588 - Synonymous.Female
589 - Synonymous.Recurrent
590 - Synonymous.Triple
591
592enrichment:
593 enabled: false
594 selected_person_set_collections:
595 - phenotype
596 selected_background_models:
597 - hg38/enrichment/coding_length_ref_gene_v20170601
598 - enrichment/samocha_background
599 - hg38/enrichment/ur_synonymous_SFARI_SSC_WGS_2
600 - hg38/enrichment/ur_synonymous_SFARI_SSC_WGS_CSHL
601 - hg38/enrichment/ur_synonymous_w1202s766e611_liftover
602 - hg38/enrichment/ur_synonymous_iWES_v1_1
603 - hg38/enrichment/ur_synonymous_iWES_v2
604 - hg38/enrichment/ur_synonymous_iWGS_v1_1
605 - hg38/enrichment/ur_synonymous_AGRE_WG38_859
606 default_background_model: enrichment/samocha_background
607 selected_counting_models:
608 - enrichment_events_counting
609 - enrichment_gene_counting
610 counting:
611 enrichment_events_counting:
612 id: enrichment_events_counting
613 name: Counting events
614 desc: Counting events
615 enrichment_gene_counting:
616 id: enrichment_gene_counting
617 name: Counting affected genes
618 desc: Counting affected genes
619 default_counting_model: enrichment_events_counting
620 effect_types:
621 - LGDs
622 - missense
623 - synonymous
624
625gene_browser:
626 enabled: true
627 frequency_column: genome_gnomad_v3_af_percent
628 frequency_name: genome GnomAD %%
629 effect_column: effect.worst effect type
630 location_column: variant.location
631 domain_min: 0.01
632 domain_max: 100