{% extends "site_base.html" %} {% load bootstrap_tags %} {% load humanize %} {% load static %} {% block extra_head %} {% endblock %} {% load i18n %} {% load sorting_tags %} {% load pagination_tags %} {% load filter_extras %} {% block head_title %}{% trans "Filter Analysis" %}{% endblock %} {% block body %}
Father Mother Child
{{ form.father }} {{ form.mother }} {{ form.child }}
Inheritance Model:
{{ form.trio_option }}
{{ form.remove_not_in_parents }} {{ form.remove_not_in_parents.label }}
Select Variants From Exclude Variants From
{{ form.individuals.errors }}{{ form.individuals.label }}:
{{ form.individuals }}
{{ form.snp_list.errors }} {{ form.snp_list.label }}:
{{ form.snp_list }}
{{ form.groups.label }}:
{{ form.groups }}
{{ form.gene_list.errors }} {{ form.gene_list.label }}:
{{ form.gene_list }}
{{ form.exclude_individuals.errors }} {{ form.exclude_individuals.label }}:
{{ form.exclude_individuals }}
{{ form.exclude_snp_list.label }}:
{{ form.exclude_snp_list }}
{{ form.exclude_groups.label }}:
{{ form.exclude_groups }}
{{ form.exclude_gene_list.errors }} {{ form.exclude_gene_list.label }}:
{{ form.exclude_gene_list }}
{{ form.mutation_type.errors }} {{ form.mutation_type.label }}:
{{ form.mutation_type }}
{{ form.chr.errors }} {{ form.chr.label }}:
{{ form.chr }}
{{ form.pos.errors }} {{ form.pos.label }}:
{{ form.pos }}
Variant Effect Functional Class Impact
{{ form.variant_type }} {{ form.func_class }} {{ form.impact }}
{{ form.dbsnp_option.label }}:
{{ form.dbsnp_option }} {{ form.dbsnp_build }}
{{ form.read_depth_option.errors }} {{ form.read_depth_option.label }}:
{{ form.read_depth_option }} {{ form.read_depth.errors }}{{ form.read_depth }}
{{ form.variants_per_gene_option.errors }} {{ form.variants_per_gene_option.label }}:
{{ form.variants_per_gene_option }} {{ form.variants_per_gene.errors }}{{ form.variants_per_gene }}
{{ form.genes_in_common.errors }} {{ form.genes_in_common }} {{ form.genes_in_common.label }}
{{ form.dbsnp.errors }} {{ form.dbsnp }} {{ form.dbsnp.label }}
{{ form.cln.errors }} {{ form.cln }} {{ form.cln.label }}
{% for filterconfig in filterconfigs %} {% endfor %}
Name User Created on Options
{{ filterconfig.name }} {{ filterconfig.user }} {{ filterconfig.created }} EditDelete
{% for filteranalysis in filteranalysis %} {% endfor %}
Name User Created on Options
{{ filteranalysis.name }} {{ filteranalysis.user }} {{ filteranalysis.created }} EditDelete
1000Genomes Frequency {{ form.genomes1000_option }} {{ form.genomes1000.errors }}{{ form.genomes1000 }}
dbSNP Frequency {{ form.dbsnp_freq_option }} {{ form.dbsnp_frequency.errors }}{{ form.dbsnp_frequency }}
Exome Variation Server Frequency {{ form.variationserver_option }} {{ form.variationserver_frequency.errors }}{{ form.variationserver_frequency }}
Sift Score {{ form.sift_option }} {{ form.sift.errors }}{{ form.sift }}
{{ form.sift_exclude.errors }} {{ form.sift_exclude }}{{ form.sift_exclude.label }}
Polyphen Score {{ form.polyphen_option }} {{ form.polyphen.errors }}{{ form.polyphen }}
{{ form.polyphen_exclude.errors }} {{ form.polyphen_exclude }}{{ form.polyphen_exclude.label }}

Example of genotype information:

0/1:0.45:10,12:22:99:211,0,262

GT:AB:AD:DP:GQ:PL

GT: Genotype

Genotype, encoded as allele values separated by either of ”/” or “|”. The allele values are 0 for the reference allele (what is in the REF field), 1 for the first allele listed in ALT, 2 for the second allele list in ALT and so on. For diploid calls examples could be 0/1, 1|0, or 1/2, etc. For haploid calls, e.g. on Y, male non-pseudoautosomal X, or mitochondrion, only one allele value should be given; a triploid call might look like 0/0/1. If a call cannot be made for a sample at a given locus, ”.” should be specified for each missing allele in the GT field (for example "./." for a diploid genotype and "." for haploid genotype). The meanings of the separators are as follows (see the PS field below for more details on incorporating phasing information into the genotypes)

AB: Allele balance for each het genotype

The allele balance (fraction of ref bases over ref + alt bases) across all bialleleic het-called samples

AD: Allelic depths for the ref and alt alleles in the order listed

The depth of coverage of each VCF allele in this sample.

DP: Read Depth (only filtered reads used for calling) GQ: Genotype Quality

Conditional genotype quality, encoded as a phred quality -10log_10p(genotype call is wrong, conditioned on the site's being variant) (Float)

PL: Normalized, Phred-scaled likelihoods for genotypes as defined in the VCF specification

The phred-scaled genotype likelihoods rounded to the closest integer (and otherwise defined precisely as the GL field) (Integers)

Open result in a new window
Genes:
{% for gene in summary.genes %} {{ gene.gene_name }}, {% endfor %}
Reset Filter {% if query_string %} | Save Config | Save Analysis {% endif %}

{%if summary.n_variants %}

Summary

Number of Variants: {{ summary.n_variants }}
Number of Genes: {{ summary.n_genes }}

{% endif %}
{% if variants %} Export to: CSVTXT {% autosort variants %} {% regroup variants.object_list by gene_name as gene_list %} {% for gene in gene_list %} {% if gene.grouper %} {% endif %} {% for variant in gene.list %} {% endif %} {% endfor %} {% endfor %}
{% anchor individual Individual %} {% anchor chromossome Chr %} {% anchor id RsId %} {% anchor pos Pos %} {% anchor qual Qual %} {% anchor ref Ref %} {% anchor alt Alt %} {% anchor genotype Gen %} {% anchor father Father %} {% anchor mother Mother %} {% anchor read_depth "Read Depth" %} {% anchor snp_eff "Mutation Type"" %} {% anchor snp_eff_functional_class "Protein Impact" %} {% anchor impact "SnpEff Class" %} {% anchor genomes1k_maf "1kgenomes" %} {% anchor dbsnp_gmaf "dbSNP137" %} {% anchor ann_esp_maf "ESP6500" %} {% anchor sift Sift %} {% anchor polyphen Polyphen %} Other Info

{{ gene.grouper }}

Omim - GeneCards - NCBI
{{ variant.individual }} {{ variant.chromossome }} {{ variant.variant_id }} {% if variant.variant_id != "." %}
dbSNP
{{ variant.pos }} {{ variant.qual }} {{ variant.ref }} {{ variant.alt }} {{ variant.genotype }} {{ variant.father }} {{ variant.mother }} {{ variant.read_depth }} {{ variant.snp_eff|cleanstr }} {{ variant.snp_eff_functional_class }} {{ variant.impact }} {% if variant.genomes1k_maf != None %} {{ variant.genomes1k_maf }} {% endif %} {{ variant.gmaf_dbsnp135|floatformat:5|intcomma }} {{ variant.ann_esp_maf|floatformat:5|intcomma }} {{ variant.sift|floatformat:2 }} {{ variant.polyphen|floatformat:2 }} View More
{% endif %} {% endblock %} {% block extra_js %} {% for variant in variants.object_list %} {% endfor %} {% endblock %}