{% extends "layout.html" %} {% from "utils.html" import comments_panel, pedigree_panel %} {% block title %} {{ super() }} - {{ institute.display_name }} - {{ case.display_name }} - {{ variant.display_name }} {% endblock %} {% block top_nav %}
  • {{ institute.display_name }}
  • {{ case.display_name }}
  • {{ variant.variant_type|capitalize }} structural variants
  • {% endblock %} {% block top_nav_right %}
  • {{ pin_button() }}
  • {{ causative_button() }}
  • {{ super() }} {% endblock %} {% block content_main %} {% if variant.missing_data %}
    Showing only first 30 genes!
    {% 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 %}
    {{ genes(variant) }}
    {{ overlapping(overlapping_snvs, variant.rank_score) }}
    {{ ext_links(variant) }}
    {% endblock %} {% macro pin_button() %} {% if variant._id not in case.suspects %}
    {% else %}
    {% endif %} {% endmacro %} {% macro causative_button() %} {% if variant._id in case.causatives %}
    {% else %}
    {% endif %} {% endmacro %} {% macro frequencies(variant) %}
    Frequencies
    {% endmacro %} {% macro gt_calls(samples) %}
    {% for sample in samples %} {% for allele in sample.allele_depths %} {% endfor %} {% endfor %}
    Sample Genotype Alleles GQ
    1st 2nd
    {{ sample.display_name }} {{ sample.genotype_call }}{{ allele }}{{ sample.genotype_quality }}
    {% if variant.callers %} {% endif %}
    {% endmacro %} {% macro genes(variant) %}
    Genes
    {% for gene in variant.genes %} {% endfor %}
    Gene Ensembl Region Function Description OMIM
    {{ gene.common.hgnc_symbol }} {{ gene.common.ensembl_id }} {{ gene.region_annotation }} {{ gene.functional_annotation }} {{ gene.common.description|replace('_', ' ') }} {% if gene.common.omim_id %} {{ gene.common.omim_id }} {% endif %}
    {% endmacro %} {% macro ext_links(variant) %} {# External links #}
    Ensembl UCSC DECIPHER
    {% endmacro %} {% macro overlapping(other_variants, rank_score) %}
    Overlapping SNVs
    {% for variant in other_variants %} {% else %} {% endfor %}
    Variant Gene Combined score Rank score Region Function
    {{ 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(',') }}
    No overlapping SNVs found
    {% endmacro %}