{% 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 %} {% endblock %} {% block top_nav_right %} {% if config['MAIL_USERNAME'] %} {# Email setting must be setup #} {% endif %} {{ super() }} {% endblock %} {% block content_main %} {% if variant.missing_data %}
Showing only first 30 genes!
{% endif %}
  • Rank {{ variant.variant_rank }}
  • Rank score {{ variant.rank_score }}
  • Category {{ variant.sub_category|upper }}
  • Gene panels
  • Position
    {{ variant.chromosome }}:{{ variant.position }} {{ "-" if variant.end_chrom == variant.chromosome else " / "+variant.end_chrom+":" }}{{ variant.end }}
  • Breakpoint 1
    {{ variant.chromosome }}:{{ variant.position }} {% if variant.chromosome == "MT" and case.mt_bams %} - Alignment: IGV viewer {% elif case.bam_files %} - Alignment: IGV {% else %} - BAM file(s) missing {% endif %} - UCSC
  • Breakpoint 2
    {{ variant.end_chrom }}:{{ variant.end }} {% if variant.end_chrom == "MT" and case.mt_bams %} - Alignment: IGV viewer {% elif case.bam_files %} - Alignment: IGV {% else %} - BAM file(s) missing {% endif %} - UCSC
  • 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
    {{ variant.length }} {% if variant.chromosome == "MT" and case.mt_bams %} - Alignment: IGV viewer {% elif case.bam_files and variant.chromosome == variant.end_chrom %} - Alignment: IGV {% elif case.bam_files %} - Complex rearrangement: check breakpoint alignments. {% else %} - BAM file(s) missing {% endif %} {% if variant.chromosome == variant.end_chrom %} - UCSC {% endif %}
  • 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 %}
{{ 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_snvs, variant.rank_score) }}
{{ ext_links(variant) }}
{% 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 %} {% 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_panel(variant) %}
{% for gene in variant.genes %} {% if gene.common %} {% else %} {% endif %} {% endfor %}
Gene Ensembl Region Function Description OMIM
{{ gene.common.hgnc_symbol if gene.common else gene.hgnc_id }} {{ gene.common.ensembl_id }} {{ gene.region_annotation }} {{ gene.functional_annotation }} {{ gene.common.description|replace('_', ' ') }} {% if gene.common.omim_id %} {{ gene.common.omim_id }} {% endif %} {{ gene.hgnc_id }} {{ gene.region_annotation }} {{ gene.functional_annotation }}
{% endmacro %} {% macro transcripts_panel() %}
{% for gene in variant.genes %} {% for transcript in gene.transcripts %} {% endfor %} {% endfor %}
Gene Transcript RefSeq Biotype Mutation type Strand Exon Intron
{{ 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 '' }}
{% endmacro %} {% macro ext_links(variant) %} {# External links #}
Ensembl 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 %} {% macro verify_button() %} {% if variant.sanger_ordered %} {% if variant.validation in ['True positive', 'False positive']%} {% else %} {% endif %} {% else %} {% endif %} {% endmacro %} {% macro verify_modal() %}
{% endmacro %} {% macro modal_cancel_verify() %}
{% endmacro %} {% macro verify_form() %} {% endmacro %} {% block scripts %} {{ super() }} {% endblock %}