{% if query %}
Name | Value |
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 %}
|
# |
RSID |
Symbol |
C |
Samples |
Effect |
Het |
Alt |
Qual |
AF |
Location |
Impact |
IGV |
UCSC |
1000G (HG19) |
OMIM |
ExAC (HG19) |
gnomAD (HG19) |
{% for r in results %}
+ |
{{ 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}} |
{% if r.typ < 4 %}
{{ r.ref }}>{{ "ACGT"[r.typ] }} |
{% else %}
|
{% endif %}
{{ r.maxqual }} |
{{ (r.minaf) | round(2) }} - {{ (r.maxaf) | round(2) }} |
{{ r.chrom }}:{{ r.position }} |
{{ ["MODIFIER", "LOW", "MODERATE", "HIGH"][r.maximpact] }} |
{% 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%}
{% if homhetdata and caseslist %}
Legend:
het |
hom |
both |
Heterozygot |
Homozygot |
Both |
|
Count |
{% for sample in caseslist %}
{{ sample }} |
{% endfor %}
{%- for gene in homhetdata -%}
{{ gene }}
|
{{ homhetdata[gene]|length }}
|
{%- for sample in caseslist -%}
{{ homhetdata[gene][sample] }} |
{% endfor %}
{% endfor %}
{% 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 %}