{% macro rankscore_panel(variant) %}
Rank score results
{% for result in variant.rank_score_results %} {% endfor %} {% for result in variant.rank_score_results %} {% endfor %}
{{ result.category|replace('_', ' ') }}
{{ result.score }}
{% endmacro %} {% macro overlapping_panel(variant, overlapping_vars, case, institute) %}
{% if variant.category == 'sv' %}
Overlapping SNVs
{% else %}
Overlapping SVs
{% endif %}
{% for overlapping_variant in overlapping_vars %} {% else %} {% endfor %}
Variant Gene Type Combined score Rank score Length Region Function
{{ overlapping_variant.display_name|truncate(20, True) }} {{ overlapping_variant.hgnc_symbols|join(', ')|truncate(40, True) }} {{ overlapping_variant.sub_category|upper }} {{ variant.rank_score + overlapping_variant.rank_score }} {{ overlapping_variant.rank_score }} {{ overlapping_variant.length }} {{ overlapping_variant.region_annotations|join(', ')|truncate(40, True) }} {{ overlapping_variant.functional_annotations|join(', ')|truncate(40, True) }}
No overlapping variants found
{% endmacro %} {% macro genes_panel(variant) %}
{% for gene in variant.genes %} {% endfor %}
Gene Ensembl ID Description
{{ gene.common.hgnc_symbol if gene.common else gene.hgnc_id }} {% if gene.common %} {{ gene.common.ensembl_id }} {% endif %} {{ gene.common.description if gene.common }}
{% endmacro %} {% macro transcripts_panel(variant) %}
{% for gene in variant.genes %} {% for transcript in gene.transcripts %} {% endfor %} {% endfor %}
Gene Transcript RefSeq Biotype Mutation type Strand Exon Intron cDNA Amino acid
{{ 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 '' }} {{ (transcript.coding_sequence_name or '') }} {{ (transcript.protein_sequence_name or '')|url_decode }}
{% endmacro %} {% macro proteins_panel(variant) %}
{% for gene in variant.genes %} {% for transcript in gene.transcripts %} {% endfor %} {% endfor %}
Gene Transcript Protein SWISS PROT Sift Polyphen Pfam ProSite Smart
{{ gene.common.hgnc_symbol if gene.common else gene.hgnc_id }} {{ transcript.transcript_id }} {{ transcript.protein_id if transcript.protein_id }} {% if transcript.swiss_prot != 'unknown' %} {{ transcript.swiss_prot }} {% else %} {{ transcript.swiss_prot }} {% endif %} {{ transcript.sift_prediction }} {{ transcript.polyphen_prediction }} {{ transcript.pfam_domain if transcript.pfam_domain }} {{ transcript.prosite_profile if transcript.prosite_profile }} {{ transcript.smart_domain if transcript.smart_domain }}
{% endmacro %} {% macro sv_alignments(variant, case, zoom)%}
{% if zoom == "start" %} {{ variant.chromosome }}:{{ variant.position }} {% elif zoom == "end" %} {{ variant.chromosome }}:{{ variant.end }} {% elif zoom == "length" %} {{ variant.length }} {% endif %}
{% if case.mt_bams or case.bam_files %} {% if zoom == "start" %} {% elif zoom == "end" %} {% elif zoom == "length" %} {% endif %} {% endif %} {% if variant.chromosome == "MT" and case.mt_bams %} - Alignment: {% elif case.bam_files %} - Alignment: {% if case.rhocall_beds %} {% endif %} {% if case.tiddit_coverage_wigs %} {% endif %} {% if case.upd_regions_beds %} {% endif %} {% if case.upd_sites_beds %} {% endif %} {% if zoom == "length" and variant.chromosome != variant.end_chrom %} - Complex rearrangement: check breakpoint alignments. {% else %} {% endif %} {% else %} - BAM file(s) missing {% endif %} {% if zoom == "length" and variant.chromosome == variant.end_chrom %} - UCSC {% elif zoom == "start" %} - UCSC {% elif zoom == "end" %} - UCSC {% endif %}
{% endmacro %} {% macro pin_button(variant, case, institute) %} {% if variant._id not in case.suspects %}
{% else %}
{% endif %} {% endmacro %} {% macro causative_button(variant, case, institute) %} {% if variant._id in case.causatives %}
{% elif variant._id in case.partial_causatives %}
{% else %} {% endif %} {% endmacro %}