{% macro modal_causative(case, institute, variant) %} {% endmacro %} {% macro igv_track_selection(igv_tracks, current_user) %}
Show tracks:
{% 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
{% if overlapping_variant.category in ("sv", "cancer_sv") %} {{ overlapping_variant.display_name|truncate(20, True) }} {% else %} {{ overlapping_variant.display_name|truncate(20, True) }} {% endif %} {{ 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)%} {% set align_start = variant.position - 500 if variant.position > 500 else 0 %} {% set align_end = variant.end + 500 %} {% set chrom = variant.chromosome %}
{% if zoom == "start" %} {% set align_end = variant.position + 500 %} {{variant.chromosome}}:{{variant.position|human_longint|safe}} {% elif zoom == "end" %} {% set align_start = variant.end - 500 %} {% set chrom = variant.end_chrom %} {{variant.end_chrom}}:{{variant.end|human_longint|safe}} {% elif zoom == "length" %} {{ '-' if variant.length == 100000000000 else variant.length|human_longint|safe }} {% endif %}
{% if variant.is_mitochondrial and case.mt_bams or case.bam_files %} IGV viewer {% else %} - BAM file(s) missing {% endif %}
{% set build = "hg19" %} {% if case.genome_build == 38 or variant.chromosome == "MT" %} {% set build = "hg38" %} {% 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 'suspects' in case and case.suspects and variant._id in case.suspects %}
{% else %}
{% endif %} {% endmacro %} {% macro causative_button(variant, case, institute) %} {% if 'causatives' in case and case.causatives and variant._id in case.causatives %}
{% elif 'partial_causatives' in case and case.partial_causatives and variant._id in case.partial_causatives %}
{% else %} {% endif %} {% endmacro %}