{% macro gtcall_panel(variant) %}
GT call {% if variant.is_par %} PAR {% endif %}
{% if variant.category == "cancer" %} {% elif variant.category == "sv" %} {% elif variant.category == "str" %} {% else %} {% if variant.chromosome in ["MT","M"] %} {% endif %} {% endif %} {% for sample in variant.samples %} {% if sample.allele_depths %} {% for number in sample.allele_depths %} {% endfor %} {% else %} {% endif %} {% if variant.category == "snv" and variant.chromosome in ["MT","M"] %} {% endif %} {% if variant.category == "cancer" %} {% set cancer_var = namespace() %} {% if variant.tumor and sample.sample_id == variant.tumor.ind_id %} {% set cancer_var.vaf = variant.tumor.alt_freq|round(4) %} {% elif variant.normal and sample.sample_id == variant.normal.ind_id %} {% set cancer_var.vaf = variant.normal.alt_freq|round(4) %} {% else %} {% set cancer_var.vaf = "N/A" %} {% endif %} {% else %} {% endif %} {% endfor %}
Sample Genotype (GT) Allele depth (AD)Variant Allele Frequency (VAF)SV qualityExpansionHunter supportVariant Allele Frequency (VAF)Genotype quality (GQ)
Reference Alternative
{{ sample.display_name }} {{ sample.genotype_call }} {% if number == -1 %} N/A {% else %} {{ number }} {% endif %} N/A N/A {% if sample.alt_frequency and sample.alt_frequency != -1 %} {{ (100*sample.alt_frequency)|round(2) }}% {% else %} N/A {% endif %} {{ cancer_var.vaf }} {% if variant.category == "sv" %} {% if sample.genotype_quality not in ["None", None, "-1", -1] %} {{ sample.genotype_quality }} {% else %} N/A {% endif %} (VQ {% if variant.quality not in ["None", None, "-1", -1] %} {{variant.quality}} {% else %} N/A {% endif%}) {% elif variant.category == "str" %} {{ sample.so }} {% else %} {{ sample.genotype_quality }} {% endif %}
{% endmacro %} {% macro frequencies(variant) %}
Frequencies
{% for freq_name, value, link in variant.frequencies %} {% endfor %}
Source Frequency
{% if link %} {{ freq_name }} {% else %} {{ freq_name }} {% endif %} {% if value %} {{ value|human_decimal }} {% else %} - {% endif %}
{% endmacro %} {% macro observations_panel(variant, observations, case) %}
Local observations ?
{% for loqusid, obs in observations.items() %} {% if obs.cases %} {% endif %} {% endfor %}
ID Nr obs. Nr homo. Total nr.
{{ loqusid }} {{ obs.observations|default('N/A') }} {{ obs.homozygote|default('N/A') }} {{ obs.total|default('N/A') }}
{% for data in obs.cases %} {% if data.variant and data.variant.category == "snv"%} {{ data.case.display_name }} {% elif data.variant and data.variant.category == "sv"%} {{ data.case.display_name }} {% else %} {{ data.case.display_name }} {% endif %} {% endfor %} {% if obs.cases|length > 10 %} + more {% endif %} {% if obs.observations == 1 %} Observed only in this case {% endif %}
{% endmacro %} {% macro old_observations(variant, obs_date) %} {% if "SHOW_OBSERVED_VARIANT_ARCHIVE" in config and config["SHOW_OBSERVED_VARIANT_ARCHIVE"] == true %}
Local observations (archive {{ obs_date or variant.local_obs_old_date or "version"}})
{% if variant.category in ['cancer', 'cancer_sv'] %} {% endif %}
Archive Nr obs. Nr homo. Frequency
RD {{ variant.local_obs_old|default('N/A') }} {{ variant.local_obs_hom_old|default('N/A') }} {% if variant.local_obs_old_freq %} {{variant.local_obs_old_freq|round(6)}} {% elif variant.local_obs_old_nr_cases and variant.local_obs_old %} {{ (variant.local_obs_old/variant.local_obs_old_nr_cases)|round(5) }} {% elif variant.local_obs_old_nr_cases %} 0 / {{variant.local_obs_old_nr_cases}} {% else %} N/A {% endif %}
Cancer Germline {{ variant.local_obs_cancer_germline_old|default('N/A') }} {{ variant.local_obs_cancer_germline_hom_old|default('N/A') }} {% if variant.local_obs_cancer_germline_old_freq %} {{variant.local_obs_cancer_germline_old_freq|round(6)}} {% elif variant.local_obs_cancer_germline_old_nr_cases and variant.local_obs_cancer_germline_old %} {{ (variant.local_obs_cancer_germline_old/variant.local_obs_cancer_germline_old_nr_cases)|round(5) }} {% elif variant.local_obs_cancer_germline_old_nr_cases %} 0 / {{variant.local_obs_cancer_germline_old_nr_cases}} {% else %} N/A {% endif %}
Cancer Somatic {{ variant.local_obs_cancer_somatic_old|default('N/A') }} {{ variant.local_obs_cancer_somatic_hom_old|default('N/A') }} {% if variant.local_obs_cancer_somatic_old_freq %} {{variant.local_obs_cancer_somatic_old_freq|round(6)}} {% elif variant.local_obs_cancer_somatic_old_nr_cases and variant.local_obs_cancer_somatic_old %} {{ (variant.local_obs_cancer_somatic_old/variant.local_obs_cancer_somatic_old_nr_cases)|round(5) }} {% elif variant.local_obs_cancer_somatic_old_nr_cases %} 0 / {{variant.local_obs_cancer_somatic_old_nr_cases}} {% else %} N/A {% endif %}
{% endif %} {% endmacro %} {% macro severity_list(variant) %}
Severity
{% endmacro %} {% macro conservations(variant) %}
Conservation
{% endmacro %} {% macro mappability_list(variant) %} {% set superdups_fracmatches = [] %} {% for gene in variant.genes %} {% for transcript in gene.transcripts %} {% if transcript.superdups_fracmatch %} {% for superdup in transcript.superdups_fracmatch %} {% do superdups_fracmatches.append(superdup) %} {% endfor %} {% endif %} {% endfor %} {% endfor %} {% set superdups_fracmatches = superdups_fracmatches|sort %} {% if superdups_fracmatches %}
  • mapping to {{superdups_fracmatches|length}} segm. dups. (min matching:{{ superdups_fracmatches|first|float|round(3) }}, max matching:{{ superdups_fracmatches|last|float|round(3) }})
  • {% else %}
  • -

  • {% endif %} {% endmacro %} {% macro mappability(variant) %}
    Mappability (fracMatch)
    {% endmacro %}