{% if variant.category == "fusion" %}
{{ fusion_variant_gene_symbols_cell(variant) }}
{% else %}
{{ variant_gene_symbols_cell(variant) }}
{% endif %}
|
{% set var_type_page = {"snv":"variant.variant", "str":"variant.variant", "mei": "variant.variant", "cancer":"variant.cancer_variant", "sv":"variant.sv_variant", "cancer_sv": "variant.sv_variant", "fusion": "variant.variant"} %}
{% for key, page in var_type_page.items() %}
{% if variant.category == key %}
{{ variant.display_name|truncate(15, True) }}
{% endif %}
{% endfor %}
|
{% if variant.category in 'str' %}
{{ variant.alternative|truncate(10, True) | replace("<", " ") | replace(">", "")}}
{% else %}
{{ variant.reference|truncate(10, True) }} → {{ variant.alternative|truncate(10, True) }}
{% endif%}
|
{% if variant.first_rep_gene and variant.first_rep_gene.hgvs_identifier %}
{{variant.first_rep_gene.hgvs_identifier|truncate(15, True)}}
{% else %}
-
{% endif %}
|
{% if variant.first_rep_gene and variant.first_rep_gene.hgvsp_identifier %}
{{variant.first_rep_gene.hgvsp_identifier|truncate(15, True)}}
{% else %}
-
{% endif %}
|
{{ variant_funct_anno_cell(variant) }}
|
{{ variant.category|upper }}
|
{% for key, values in callers.items() %}
{% if variant.category == key %}
{% for caller in values %}
{% if caller.id in variant %}
{{caller.name}}:{{variant[caller.id]}}
{% endif %}
{% endfor %}
{% endif %}
{% endfor %}
|
{% if variant.cadd_score %}
{{ variant.cadd_score|round(2) }}
{% else %}
-
{% endif %}
|
{{ variant.rank_score }}
{% if variant.category == 'sv' %}
(v. {{case.sv_rank_model_version or 'na'}})
{% else %}
(v. {{case.rank_model_version or 'na'}})
{% endif %}
|
{% for score in [variant.revel, variant.revel_score] %}
{% if score %}
{{score|round(2)}}
{% else %}
-
{% endif %}
|
{% endfor %}
{{ variant.spliceai_scores|list_remove_none|join(', ') if variant.spliceai_scores else "-" }}
|
{%- for sample in variant.samples -%}
{%- for ind in case.individuals -%}
{%- if sample.sample_id == ind.individual_id -%}
{% if sample.genotype_call not in ['0/0', './.', '0/.', './0'] %}
{% do analysis_types.append(ind.analysis_type) %}
{% endif %}
{% set allele_depths = ['ref depth', sample.allele_depths[0]]|join(":") + ' - ' + ['alt depth', sample.allele_depths[1]]|join(":") %}
{{sample.genotype_call}} GQ:{{sample.genotype_quality}} AD:{{sample.allele_depths[0]}}|{{sample.allele_depths[1]}}
{%- endif -%}
{%- endfor -%}
{%- endfor -%}
|
{% for model in variant.genetic_models %}
{{model}}
{% endfor %}
|
{% if 'acmg_classification' in variant %}
{{acmg_map[variant.acmg_classification].short}}
{% else %}
-
{% endif %}
|
{{ case.display_name }}
{{ case.status }}
{% if (case.partial_causatives and variant._id in case.partial_causatives) %}
partial
{% endif %}
|
{{ analysis_type(analysis_types|unique) }}
|
{% if variant.validation %}
{{ variant.validation }}
{% endif %}
|
{% endfor %}