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config_AnnotSV.yaml
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config_AnnotSV.yaml
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##############################################################################################
# knotAnnotSV 1.1 #
# #
# knotAnnotSV: Creation of a customizable html file to visualize, filter #
# and analyze an AnnotSV output #
# #
# Author: Thomas Guignard 2020-present #
# #
# Copyright (C) 2020-present Thomas Guignard (t-guignard@chu-montpellier.fr) #
# #
# This is part of knotAnnotSV source code. #
# #
# This program is free software; you can redistribute it and/or #
# modify it under the terms of the GNU General Public License #
# as published by the Free Software Foundation; either version 3 #
# of the License, or (at your option) any later version. #
# #
# This program is distributed in the hope that it will be useful, #
# but WITHOUT ANY WARRANTY; without even the implied warranty of #
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the #
# GNU General Public License for more details. #
# #
# You should have received a copy of the GNU General Public License #
# along with this program; If not, see <http://www.gnu.org/licenses/>. #
##############################################################################################
---
#### General annotations on the SV
##################################
AnnotSV_ID: #mandatory in first position
POSITION: 1
RENAME: "AnnotSV ID"
ACMG_class: # mandatory
POSITION: 2
RENAME: "ACMG class"
HEADERTIPS: "SV ranking class (from 1 to 5) following the 2020 joint consensus recommendation of ACMG and ClinGen"
COMMENTLIST:
- AnnotSV_ranking_score
- AnnotSV_ranking_criteria
SV_type:
POSITION: 3
RENAME: "SV type"
HEADERTIPS: "Type of the SV (DEL, DUP...)"
COMMENTLIST:
- SV_length
- Gene_count
Annotation_mode: #mandatory
POSITION: 4
RENAME: "Annotation mode"
HEADERTIPS: "Type of annotation lines generated:<br>
- annotation on the SV full length (full)<br>
- annotation on each gene overlapped by the SV (split)"
### Gene annotations
####################
Gene_name: # mandatory
POSITION: 5
RENAME: "Gene name"
HEADERTIPS: "Gene symbol"
COMMENTLIST:
- LOEUF_bin
- GnomAD_pLI
- ExAC_pLI
- HI
- TS
- DDD_HI_percent
- ACMG
- ExAC_cnvZ
- ExAC_delZ
- ExAC_dupZ
- ExAC_synZ
- ExAC_misZ
- GenCC_disease
- GenCC_moi
- GenCC_classification
- GenCC_pmid
- Closest_left
- Closest_right
- NCBI_gene_ID
Location:
POSITION: 6
RENAME: "Location"
HEADERTIPS: "Hover your mouse to highlight SV location annotations in the gene"
COMMENTLIST:
- CytoBand
- Location2
- Tx
- Tx_version
- Tx_start
- Tx_end
- Exon_count
- Overlapped_tx_length
- Overlapped_CDS_length
- Overlapped_CDS_percent
- Frameshift
- Dist_nearest_SS
- Nearest_SS_type
- Intersect_start
- Intersect_end
OMIM_ID:
POSITION: 7
RENAME: "OMIM ID"
HEADERTIPS: "Hover your mouse to highlight OMIM annotations"
COMMENTLIST:
- OMIM_phenotype
- OMIM_inheritance
- OMIM_morbid
- OMIM_morbid_candidate
Exomiser_gene_pheno_score:
POSITION: 8
RENAME: "Exomiser score"
HEADERTIPS: "Show how close each overlapped gene is to the patient phenotype<br>
Highly specific and consistent phenotype: score > 0.7<br>
Consistent phenotype: score > 0.5"
COMMENTLIST:
- Human_pheno_evidence
- Mouse_pheno_evidence
- Fish_pheno_evidence
PhenoGenius_specificity:
POSITION: 9
RENAME: "PhenoGenius specificity"
HEADERTIPS: "Phenotype specificity into one of A, B, C, D or . :<br>
A - Highly specific and relatively unique to the gene<br>
B - Consistent with the gene, highly specific, but not necessarily unique to the gene<br>
C - Limited association with the gene, not highly specific and/or with high genetic heterogeneity<br>
D - Not consistent with what is expected for the gene/genomic region or not consistent in general<br>
. - No reported phenotype"
COMMENTLIST:
- PhenoGenius_phenotype
- PhenoGenius_score
### Annotations done with regulatory elements
#############################################
RE_gene:
POSITION: 10
RENAME: "Overlapped regulatory elements"
HEADERTIPS: "Report the name of the genes potentially badly regulated"
### Annotations done with pathogenic SV
#######################################
P_gain_coord:
POSITION: 11
RENAME: "Pathogenic SV"
HEADERTIPS: "Known pathogenic genes or genomic regions (with the same SV type; from ClinVar, ClinGen, dbVar, OMIM) completely overlapped with the SV to annotate"
COMMENTLIST:
- P_gain_source
- P_gain_phen
- P_gain_hpo
- P_loss_coord
- P_loss_source
- P_loss_phen
- P_loss_hpo
- po_P_gain_phen
- po_P_gain_hpo
- po_P_gain_source
- po_P_gain_coord
- po_P_gain_percent
- po_P_loss_phen
- po_P_loss_hpo
- po_P_loss_source
- po_P_loss_coord
- po_P_loss_percent
### Annotations done with pathogenic snv/indel
##############################################
P_snvindel_nb:
POSITION: 12
RENAME: "Number of pathogenic SNV/indel overlapped"
HEADERTIPS: "Pathogenic SNV/indel (from ClinVar) completely overlapped with the SV to annotate"
COMMENTLIST:
- P_snvindel_phen
### Annotations done with benign SV
###################################
B_gain_source:
POSITION: 13
RENAME: "Benign SV"
HEADERTIPS: "Benign genomic regions (with the same SV type; from gnomAD, ClinVar, ClinGen, DGV, DDD, 1000g, IMH) completely overlapping the SV to annotate"
COMMENTLIST:
- B_gain_coord
- B_gain_AFmax
- B_loss_source
- B_loss_coord
- B_loss_AFmax
- po_B_gain_allG_source
- po_B_gain_allG_coord
- po_B_gain_someG_source
- po_B_gain_someG_coord
- po_B_loss_allG_source
- po_B_loss_allG_coord
- po_B_loss_someG_source
- po_B_loss_someG_coord
### Annotations of the breakpoints
##################################
ENCODE_blacklist_characteristics_left:
POSITION: 14
RENAME: "Left breakpoint annotations"
HEADERTIPS: "Hover your mouse to highlight the left SV breakpoint (+/- 100bp) annotations"
COMMENTLIST:
- ENCODE_blacklist_left
- SegDup_left
- Repeat_coord_left
- Repeat_type_left
- Gap_left
- GC_content_left
ENCODE_blacklist_characteristics_right:
POSITION: 15
RENAME: "Right breakpoint annotations"
HEADERTIPS: "Hover your mouse to highlight the right SV breakpoint (+/- 100bp) annotations"
COMMENTLIST:
- ENCODE_blacklist_right
- SegDup_right
- Repeat_coord_right
- Repeat_type_right
- Gap_right
- GC_content_right
TAD_coordinate:
POSITION: 0
ENCODE_experiment:
POSITION: 0
Cosmic_ID:
POSITION: 0
Cosmic_mut_typ:
POSITION: 0
Compound-htz(sample):
POSITION: 0
Count_hom(sample):
POSITION: 0
Count_htz(sample):
POSITION: 0
Count_htz/allHom(sample):
POSITION: 0
Count_htz/total(cohort):
POSITION: 0
Count_total(cohort):
POSITION: 0