{% macro gtcall_panel(variant) %}
GT call
{% if variant.is_par %}
PAR
{% endif %}
Sample |
Genotype (GT) |
Allele depth (AD) |
Genotype quality (GQ) |
Reference |
Alternative |
{% for sample in variant.samples %}
{{ sample.display_name }} |
{{ sample.genotype_call }} |
{% if sample.allele_depths %}
{% for number in sample.allele_depths %}
{{ number }} |
{% endfor %}
{% else %}
N/A |
N/A |
{% endif %}
{{ sample.genotype_quality }} |
{% endfor %}
{% endmacro %}
{% macro frequencies(variant) %}
Frequencies
Source |
Frequency |
{% for freq_name, value, link in variant.frequencies %}
{% if link %}
{{ freq_name }}
{% else %}
{{ freq_name }}
{% endif %}
|
{% if value %}
{{ value|human_decimal }}
{% else %}
-
{% endif %}
|
{% endfor %}
{% endmacro %}
{% macro observations_panel(variant, observations, case) %}
Nr obs. |
Nr homo. |
Total nr. |
{{ observations.observations|default('N/A') }} |
{{ observations.homozygote|default('N/A') }} |
{{ observations.total }} |
{% endmacro %}
{% macro old_observations(variant, obs_date) %}
Nr obs. |
Nr homo. |
Total nr. |
{{ variant.local_obs_old or 'N/A' }} |
{{ variant.local_obs_hom_old or 'N/A' }} |
{{ variant.local_obs_total_old or 638 }} |
{% endmacro %}
{% macro severity_list(variant) %}
Severity
-
SIFT
{{ variant.sift_predictions|join(', ') }}
-
REVEL
{{ variant.revel_score or "-" }}
-
Polyphen
{{ variant.polyphen_predictions|join(', ') }}
-
SPIDEX
{{ variant.spidex_human }}
{% endmacro %}
{% macro conservations(variant) %}
Conservation
-
PHAST
{{ variant.phast_conservation|join(', ') or '-' }}
-
GERP
{{ variant.gerp_conservation|join(', ') or '-' }}
-
phyloP
{{ variant.phylop_conservation|join(', ') or '-' }}
{% endmacro %}
{% macro mappability(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 %}