{% macro gtcall_panel(variant) %}
Sample | Genotype (GT) | Allele depth (AD) | {% if variant.category == "cancer" %}Variant Allele Frequency (VAF) | {% elif variant.category == "sv" %}SV quality | {% elif variant.category == "str" %}ExpansionHunter support | {% else %} {% if variant.chromosome in ["MT","M"] %}Variant Allele Frequency (VAF) | {% endif %}Genotype quality (GQ) | {% endif %}|
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Reference | Alternative | |||||||
{{ sample.display_name }} | {{ sample.genotype_call }} | {% if sample.allele_depths %} {% for number in sample.allele_depths %}{% if number == -1 %} N/A {% else %} {{ number }} {% endif %} | {% endfor %} {% else %}N/A | N/A | {% endif %} {% if variant.category == "snv" and variant.chromosome in ["MT","M"] %}{% if sample.alt_frequency and sample.alt_frequency != -1 %} {{ (100*sample.alt_frequency)|round(2) }}% {% else %} N/A {% endif %} | {% 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 %}{{ cancer_var.vaf }} | {% else %}{% 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 %} | {% endif %}
Source | Frequency |
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{% if link %} {{ freq_name }} {% else %} {{ freq_name }} {% endif %} | {% if value %} {{ value|human_decimal }} {% else %} - {% endif %} |
ID | Nr obs. | Nr homo. | Total nr. |
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{{ 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 %} |
Archive | Nr obs. | Nr homo. | Frequency |
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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 %} |
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