{% extends "layout.html" %} {% from "macros.html" import list_out, list_out_bytes, igv_link, igv_open_file, ucsc_link, genemania_single_link, ensemble_link, all_link %} {% block caption %}{% endblock %} {% block title %}{{ title }}{% endblock %} {% block body %}
{% if query %}
NameValue
Case {% for sample in query.case %} {{ sample }}{% if not loop.last %}, {% endif %} {% endfor %}
Case Groups {% for group in query.case_groups %} {{ group }}{% if not loop.last %}, {% endif %} {% endfor %}
Control {% for sample in query.control %} {{ sample }}{% if not loop.last %}, {% endif %} {% endfor %}
Control Groups {% for group in query.control_groups %} {{ group }}{% if not loop.last %}, {% endif %} {% endfor %}
Reference Genome {%- if query.usehg19 -%}hg19{% else %}hg38{% endif %}
min Qual {{ query.min_qual }}
min Samples per Gene {{ query.min_samples_per_gene }}
min Samples per Variant {{ query.min_samples_per_variant }}
min Variants per Gene {{ query.min_variants_per_gene }}
{% endif %}
{% for r in results %} {% if r.typ < 4 %} {% else %} {% endif %} {% if query %} {{ all_link(r.chrom, r.position, r.ref, "ACGT"[r.typ], None, r.symbols, query.usehg19) }} {% else %} {{ all_link(r.chrom, r.position, r.ref, "ACGT"[r.typ], None, r.symbols, True) }} {% endif %} {% endfor%}
# RSID Symbol C Samples Effect Het Alt Qual AF Location Impact IGV UCSC 1000G (HG19) OMIM ExAC (HG19) gnomAD (HG19)
+ {{ loop.index }} {{ r.rsid | rsid }} {% for symbol in r.symbols %} {% set s = symbol.decode() %} {{ ensemble_link(s) }}{% if not loop.last %}, {% endif %} {% endfor %} {{ r.common | length }} {% for s in r.samples %} {{ igv_open_file('bam' + "/" + s + '.bam', s) }} {% if not loop.last %}, {% endif %} {% endfor %}{{ list_out() }} {{ r.effect|effects }} {{ r.rowheterozygot|heterozygosity}}{{ r.ref }}>{{ "ACGT"[r.typ] }}{{ r.maxqual }} {{ (r.minaf) | round(2) }} - {{ (r.maxaf) | round(2) }} {{ r.chrom }}:{{ r.position }} {{ ["MODIFIER", "LOW", "MODERATE", "HIGH"][r.maximpact] }}
{% if homhetdata and caseslist %}
Legend:
het hom both
Heterozygot Homozygot Both
{% for sample in caseslist %} {% endfor %} {%- for gene in homhetdata -%} {%- for sample in caseslist -%} {% endfor %} {% endfor %}
Count
{{ sample }}
{{ gene }} {{ homhetdata[gene]|length }} {{ homhetdata[gene][sample] }}
{% endif %} {% if barchart %}
{% else %}

You need to have matplotlib installed to use this feature.

We recommend installing matplotlib-minimal from our anaconda channel. It contains only the features needed for eagle. If you need matplotlib for other applications, please install the full matplotlib and seaborn packages.

{% endif %}
{% endblock %}