{% extends "layout_bs4.html" %}
{% from "utils.html" import comments_panel, pedigree_panel %}
{% from "variants/utils.html" import modal_causative %}
{% block title %}
{{ super() }} - {{ institute.display_name }} - {{ case.display_name }} - {{ variant.display_name }}
{% endblock %}
{% block css %}
{{ super() }}
{% endblock %}
{% block top_nav %}
Position
{{ variant.chromosome }}:{{ variant.position }} {{ "-" if variant.end_chrom == variant.chromosome else " / "+variant.end_chrom+":" }}{{ variant.end }}
Breakpoint 1
{{ variant.chromosome }}:{{ variant.position }}
Breakpoint 2
{{ variant.end_chrom }}:{{ variant.end }}
Cytoband
{% if variant.chromosome == variant.end_chrom and variant.cytoband_start == variant.cytoband_end %}
{{ variant.chromosome }}{{ variant.cytoband_start }}
{% elif variant.chromosome == variant.end_chrom %}
{{ variant.chromosome }}{{ variant.cytoband_start }}{{ variant.cytoband_end }}
{% else %}
{{ variant.chromosome }}{{ variant.cytoband_start }}-{{variant.end_chrom}}{{ variant.cytoband_end }}
{% endif %}
Length
Type {{ variant.sub_category|upper }}
{% if variant._id in case.suspects and not variant.clinvar_clinsig %}
Submit to ClinVar
{% endif %}
{% if variant.clinvar_clinsig%}
Modify clinvar submission
{% endif %}
{% if variant.custom %}
Custom annotation
Value
{% for pair in variant.custom %}
{{ pair[0] }}
{{ pair[1] }}
{% endfor %}
{% endif %}
{{ frequencies(variant) }}
{{ gt_calls(variant.samples) }}
{{ comments_panel(institute, case, current_user, variant.comments, variant_id=variant._id) }}
{% set has_pedigree = case.madeline_info and case.individuals|length > 1 %}
{% if has_pedigree %}
{{ pedigree_panel(case) }}
{% endif %}
{{ overlapping(overlapping_vars, variant.rank_score) }}
{{ genes_panel(variant) }}
{{ transcripts_panel() }}
{% if config['MAIL_USERNAME'] %}
{# Email setting must be setup #}
{{ verify_modal() }}
{% endif %}
{% if config['MAIL_USERNAME'] %}
{# Email setting must be setup #}
{{ modal_cancel_verify() }}
{% endif %}
{{ modal_causative(case, institute, variant) }}
{% endblock %}
{% macro pin_button() %}
{% if variant._id not in case.suspects %}
{% else %}
{% endif %}
{% endmacro %}
{% macro causative_button() %}
{% if variant._id in case.causatives %}
{% elif variant._id in case.partial_causatives %}
{% else %}
Mark causative
{% endif %}
{% endmacro %}
{% macro frequencies(variant) %}
Frequencies
{% for freq_name, value in variant.frequencies %}
{{ freq_name }}
{% if value %}
{{ value|human_decimal }}
{% else %}
-
{% endif %}
{% endfor %}
{% if config.LOQUSDB_SETTINGS %}
{{ observations.observations|default('N/A') }} obs.
{{ observations.homozygote|default('N/A') }} homo.
{{ observations.total }} tot.
{% if observations['cases'] %}
Cases
{% for data in observations['cases'] %}
{% if data.variant %}
{{ data.case.display_name }}
{% else %}
{{ data.case.display_name }}
{% endif %}
{% endfor %}
{% endif %}
{% endif %}
{% endmacro %}
{% macro gt_calls(samples) %}
Sample
Genotype
Alleles
GQ
1st
2nd
{% for sample in samples %}
{{ sample.display_name }}
{{ sample.genotype_call }}
{% for allele in sample.allele_depths %}
{{ allele }}
{% endfor %}
{{ sample.genotype_quality }}
{% endfor %}
{% if variant.callers %}
{% endif %}
{% endmacro %}
{% macro genes_panel(variant) %}
{% endmacro %}
{% macro transcripts_panel() %}
Gene
Transcript
RefSeq
Biotype
Mutation type
Strand
Exon
Intron
{% for gene in variant.genes %}
{% for transcript in gene.transcripts %}
{{ gene.common.hgnc_symbol if gene.common else gene.hgnc_id }}
{{ transcript.transcript_id }}
{% if transcript.is_canonical %}
C
{% endif %}
{{ transcript.refseq_identifiers|join(',') }}
{{ transcript.biotype or '' }}
{{ transcript.functional_annotations
|join(', ')
|truncate(20, True) }}
{{ transcript.strand }}
{{ transcript.exon or '' }}
{{ transcript.intron or '' }}
{% endfor %}
{% endfor %}
{% endmacro %}
{% macro ext_links(variant) %}
{# External links #}
{% endmacro %}
{% macro overlapping(other_variants, rank_score) %}
Overlapping SNVs
Variant
Gene
Combined score
Rank score
Region
Function
{% for variant in other_variants %}
{{ variant.display_name|truncate(20, True) }}
{{ variant.hgnc_symbols|join(', ') }}
{{ rank_score + variant.rank_score }}
{{ variant.rank_score }}
{{ variant.region_annotations|join(',') }}
{{ variant.functional_annotations|join(',') }}
{% else %}
No overlapping SNVs found
{% endfor %}
{% endmacro %}
{% macro verify_button() %}
{% if variant.sanger_ordered %}
{% if variant.validation in ['True positive', 'False positive']%}
Validation: {{ variant.validation }}
{% else %}
Verification pending...
{% endif %}
{% else %}
Verify
{% endif %}
{% endmacro %}
{% macro verify_modal() %}
{% endmacro %}
{% macro modal_cancel_verify() %}
{% endmacro %}
{% macro verify_form() %}
Encompassing genes :
{{ variant.hgnc_symbols|join(', ') }}
Gene panels :
{{ variant.panels|join(', ') }}
GT call
{% for individual in variant.samples %}
{{ individual.display_name }}: {{ individual.genotype_call }}
{% endfor %}
Ordered by :
{{ current_user.name }}
{% endmacro %}
{% block scripts %}
{{ super() }}
{% endblock %}