{% extends "layout.html" %} {% from "variants/components.html" import external_scripts, external_stylesheets, gene_cell, frequency_cell_general, observed_cell_general %} {% from "variants/utils.html" import cancer_filters, cell_rank, pagination_footer, pagination_hidden_div, dismiss_variants_block, filter_form_footer, filter_script_main, update_stash_filter_button_status %} {% from "variants/indicators.html" import pin_indicator, causative_badge, clinical_assessments_badge, comments_badge, dismissals_badge, evaluations_badge, group_assessments_badge, matching_manual_rank, other_tiered_variants, research_assessments_badge %} {% block title %} {{ variant_type|capitalize }} somatic variants {% endblock %} {% block css %} {{ super() }} {{ external_stylesheets() }} {% endblock %} {% block top_nav %} {{ super() }} {% endblock %} {% block content_main %}
{{ pagination_hidden_div(page) }}
{{ filter_form_footer(form, result_size, total_variants, more_variants, page, variants|length, institute) }}
{% for variant in variants %} {% if variant.dismiss_variant %} {% elif 'causatives' in case and variant._id in case.causatives %} {% else %} {% endif %} {% endfor %}
Gene HGVS[c/p] Assessment Qual Rank CADD Chr pos Pop Freq Observed Type Consequence Tumor Normal
{{ pin_indicator(variant, case) }} {{ gene_cell(variant) }} {% if variant.first_rep_gene.hgvs_identifier %}
{{ variant.first_rep_gene.hgvs_identifier }}
{{ (variant.first_rep_gene.hgvsp_identifier or '') |url_decode }}
{% else %}
{{ variant.reference }}→ {% if variant.alternative | length > 5 %} {{ variant.alternative[0] }}...{{ variant.alternative[-1] }} {% else %} {{ variant.alternative }} {% endif %}
{% endif %}
{{ evaluations_badge(variant) }} {{ dismissals_badge(variant) }} {{ matching_manual_rank(variant) }} {{ research_assessments_badge(variant) }} {{ clinical_assessments_badge(variant) }} {{ group_assessments_badge(variant) }} {{ comments_badge(case, institute, variant) }} {{ causative_badge(variant, case) }} {{ other_tiered_variants(variant) }} {{ quality_cell(variant) }} {{ rank_cell(variant) }} {{ cadd_cell(variant) }} {{ position_cell(variant) }} {{ frequency_cell_general(variant) }} {{ observed_cell_general(variant) }} {{ variant.sub_category }} {% for annotation in variant.functional_annotations %}
{{ annotation }}
{% endfor %}
{{ allele_cell(variant.tumor or {}) }} {{ allele_cell(variant.normal or {}) }}
{{ dismiss_variants_block(dismiss_variant_options, institute, case, show_dismiss_block) }}
{{ pagination_footer(more_variants, page) }}
{% endblock %} {% macro actions_cell(variant) %} View {% if variant.comments %} {% endif %} {% endmacro %} {% macro rank_cell(variant) %} {% if variant.rank_score is defined %} {% if variant.rank_score <= 4 %} {% set label_class = 'secondary' %} {% elif variant.rank_score == 5 %} {% set label_class = 'info' %} {% elif variant.rank_score == 6 %} {% set label_class = 'primary' %} {% elif variant.rank_score == 7 %} {% set label_class = 'warning' %} {% elif variant.rank_score > 8 %} {% set label_class = 'danger' %} {% endif %}
{{ variant.rank_score }}
{% endif %} {% endmacro %} {% macro cadd_cell(variant) %} {% if variant.cadd_score %} {% if variant.cadd_score <= 10 %} {% set label_class = 'secondary' %} {% elif variant.cadd_score <= 20 %} {% set label_class = 'primary' %} {% elif variant.cadd_score <= 25 %} {% set label_class = 'warning' %} {% elif variant.cadd_score > 29 %} {% set label_class = 'danger' %} {% endif %}
{{ variant.cadd_score|round }}
{% endif %} {% endmacro %} {% macro quality_cell(variant) %} {% for filter in variant.filters %}
{{ filter.label }}
{% endfor %} {% endmacro %} {% macro position_cell(variant) %} {{ variant.chromosome }}:{{ variant.position }} {% endmacro %} {% macro allele_cell(allele) %} {% if 'alt_freq' in allele %} {{ allele.alt_freq|round(4) }}
{{ allele.alt_depth }} | {{ allele.ref_depth }} {% else %} N/A {% endif %} {% endmacro %} {% block scripts %} {{ super() }} {{ external_scripts() }} {{ filter_script_main(cytobands) }} {% endblock %}