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filter_form.js
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filter_form.js
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var effectGroups = {
all: [
],
nonsynonymous: [
"complex_substitution",
"direct_tandem_duplication",
"disruptive_inframe_deletion",
"disruptive_inframe_insertion",
"exon_loss_variant",
"feature_truncation",
"frameshift_elongation",
"frameshift_truncation",
"frameshift_variant",
"inframe_deletion",
"inframe_insertion",
"internal_feature_elongation",
"missense_variant",
"mnv",
"start_lost",
"stop_gained",
"stop_lost",
"structural_variant",
"transcript_ablation"
],
splicing: [
"splice_acceptor_variant",
"splice_donor_variant",
"splice_region_variant"
],
coding: [
"stop_retained_variant",
"synonymous_variant"
],
utr_intronic: [
"coding_transcript_intron_variant",
"five_prime_UTR_exon_variant",
"five_prime_UTR_intron_variant",
"three_prime_UTR_exon_variant",
"three_prime_UTR_intron_variant"
],
noncoding: [
"downstream_gene_variant",
"intergenic_variant",
"downstream_gene_variant",
"downstream_gene_variant",
"non_coding_transcript_exon_variant",
"non_coding_transcript_intron_variant",
"upstream_gene_variant"
],
nonsense: [
"frameshift_elongation",
"frameshift_truncation",
"frameshift_variant",
"start_lost",
"stop_gained",
"stop_lost",
"splice_acceptor_variant",
"splice_donor_variant",
],
};
effectGroups.all = effectGroups.nonsynonymous
.concat(effectGroups.splicing)
.concat(effectGroups.coding)
.concat(effectGroups.utr_intronic)
.concat(effectGroups.noncoding)
.concat(effectGroups.nonsense);
function updateEffectGroup(group) {
let all = _.every(effectGroups[group], function (s) { return $("#id_effect_" + s).prop("checked"); });
let none = _.every(effectGroups[group], function (s) { return !$("#id_effect_" + s).prop("checked"); });
if (all) {
$("#id_effect_group_" + group).prop("checked", true);
$("#id_effect_group_" + group).prop("indeterminate", false);
} else if (none) {
$("#id_effect_group_" + group).prop("checked", false);
$("#id_effect_group_" + group).prop("indeterminate", false);
} else {
$("#id_effect_group_" + group).prop("checked", false);
$("#id_effect_group_" + group).prop("indeterminate", true);
}
}
function updateCheckboxes(event) {
if (this.blocked) {
return;
} else {
this.blocked = true;
}
if (event !== null && $(this).attr('id').startsWith('id_effect_group_')) {
// Clicked one of the group buttons itself.
let id = $(this).attr('id').substring("id_effect_group_".length);
let checked = $(this).prop('checked');
for (value in effectGroups[id]) {
$("#id_effect_" + effectGroups[id][value]).prop("checked", checked);
}
for (group in effectGroups) {
if (group != id) {
updateEffectGroup(group);
}
}
} else {
for (key in effectGroups) {
// Clicked one of the detailed buttons.
updateEffectGroup(key);
}
}
this.blocked = false;
}
updateCheckboxes.blocked = false;
$(document).ready(function() {
updateCheckboxes(null);
$(".checkboxinput").change(updateCheckboxes);
});
function polyPhen2(gene, hgvsP) {
const regex = /^p.([A-Z])(\d+)([A-Z])$/;
const found = hgvsP.match(regex);
const seqvar1 = found[1];
const seqpos = found[2];
const seqvar2 = found[3];
var form = $('<form target="_blank" method="POST" action="http://genetics.bwh.harvard.edu/cgi-bin/ggi/ggi2.cgi">');
form.append($('<input type="hidden" name="_ggi_project" value="PPHWeb2">'));
form.append($('<input type="hidden" name="_ggi_origin" value="query">'));
form.append($('<input type="hidden" name="_ggi_target_submit" value="1">'));
form.append($('<input type="hidden" name="accid" value="' + gene + '">'));
form.append($('<input type="hidden" name="seqpos" value="' + seqpos + '">'));
form.append($('<input type="hidden" name="seqvar1" value="' + seqvar1 + '">'));
form.append($('<input type="hidden" name="seqvar2" value="' + seqvar2 + '">'));
form.appendTo('body').submit();
}
function humanSplicingFinder(gene, hgvsC) {
var form = $('<form target="_blank" method="POST" action="http://www.umd.be/HSF3/4DACTION/input_SSF">');
form.append($('<input type="hidden" name="champlibre" value="' + gene + '">'));
form.append($('<input type="hidden" name="batch" value="' + hgvsC + '">'));
form.append($('<input type="hidden" name="choix_analyse" value="ssf_batch">'));
form.append($('<input type="hidden" name="autoselect" value="yes">'));
form.append($('<input type="hidden" name="snp_select" value="no">'));
form.append($('<input type="hidden" name="showonly" value="yes">'));
form.append($('<input type="hidden" name="geneStatus" value="all">'));
form.append($('<input type="hidden" name="transcriptStatus" value="all">'));
form.append($('<input type="hidden" name="nuclposition" value="100">'));
form.append($('<input type="hidden" name="nuclposition5" value="">'));
form.append($('<input type="hidden" name="nuclposition3" value="">'));
form.append($('<input type="hidden" name="choix_bdd" value="gene_name">'));
form.append($('<input type="hidden" name="exon_number" value="">'));
form.append($('<input type="hidden" name="intron_number" value="">'));
form.append($('<input type="hidden" name="remLentext" value="2500">'));
form.append($('<input type="hidden" name="sequenceWT" value="">'));
form.append($('<input type="hidden" name="remLentextmut" value="2500">'));
form.append($('<input type="hidden" name="sequenceMut" value="">'));
form.append($('<input type="hidden" name="Firstnucleotide" value="">'));
form.append($('<input type="hidden" name="Lastnucleotide" value="">'));
form.append($('<input type="hidden" name="remLentextBP" value="100">'));
form.append($('<input type="hidden" name="sequenceBP" value="">'));
form.append($('<input type="hidden" name="MDE_sequences" value="">'));
form.append($('<input type="hidden" name="paramfulltables" value="onlyvariants">'));
form.append($('<input type="hidden" name="fenetreintron" value="yes">'));
form.append($('<input type="hidden" name="fenetretaille" value="24">'));
form.append($('<input type="hidden" name="paramimages" value="no">'));
form.append($('<input type="hidden" name="matrice_3" value="no">'));
form.append($('<input type="hidden" name="Matrice" value="PSS">'));
form.append($('<input type="hidden" name="Matrice" value="maxent">'));
form.append($('<input type="hidden" name="seuil_maxent5" value="3">'));
form.append($('<input type="hidden" name="seuil_maxent3" value="3">'));
form.append($('<input type="hidden" name="seuil_nnsplice5" value="0.4">'));
form.append($('<input type="hidden" name="seuil_nnsplice3" value="0.4">'));
form.append($('<input type="hidden" name="Matrice" value="BPS">'));
form.append($('<input type="hidden" name="Matrice" value="ESE+Finder">'));
form.append($('<input type="hidden" name="seuil_sf2" value="72.98">'));
form.append($('<input type="hidden" name="seuil_sf2_esef" value="1.956">'));
form.append($('<input type="hidden" name="seuil_sf2ig" value="70.51">'));
form.append($('<input type="hidden" name="seuil_sf2ig_esef" value="1.867">'));
form.append($('<input type="hidden" name="seuil_sc35" value="75.05">'));
form.append($('<input type="hidden" name="seuil_sc35_esef" value="2.383">'));
form.append($('<input type="hidden" name="seuil_srp40" value="78.08">'));
form.append($('<input type="hidden" name="seuil_srp40_esef" value="2.67">'));
form.append($('<input type="hidden" name="seuil_srp55" value="73.86">'));
form.append($('<input type="hidden" name="seuil_srp55_esef" value="2.676">'));
form.append($('<input type="hidden" name="Matrice" value="RESCUE+ESE">'));
form.append($('<input type="hidden" name="Matrice" value="ESE+New">'));
form.append($('<input type="hidden" name="seuil_9g8" value="59.245">'));
form.append($('<input type="hidden" name="seuil_tra2" value="75.964">'));
form.append($('<input type="hidden" name="Matrice" value="Sironi">'));
form.append($('<input type="hidden" name="seuil_sironi1" value="60">'));
form.append($('<input type="hidden" name="seuil_sironi2" value="60">'));
form.append($('<input type="hidden" name="seuil_sironi3" value="60">'));
form.append($('<input type="hidden" name="Matrice" value="Decamers">'));
form.append($('<input type="hidden" name="Matrice" value="ESS+hnRNP">'));
form.append($('<input type="hidden" name="seuil_hnrnpa1" value="65.476">'));
form.append($('<input type="hidden" name="Matrice" value="PESE">'));
form.append($('<input type="hidden" name="Matrice" value="ESR">'));
form.append($('<input type="hidden" name="Matrice" value="EIE">'));
form.appendTo('body').submit();
}
function loadBeaconWidget() {
const containerId = $(this).data("beacon-container");
const vals = containerId.split("-");
const release = vals[2];
const chromosome = vals[3];
const position = vals[4];
const reference = vals[5];
const alternative = vals[6];
const iframe = $(
'<iframe src="https://beacon-network.org:443/#/widget?rs=' + release + '&chrom=' + chromosome + '&pos=' + position + '&ref=' + reference + '&allele=' + alternative + '"\n' +
'style="width: 100%; height: 300px; overflow: auto;" \n' +
'marginwidth="0" marginheight="0" frameborder="0" vspace="0" hspace="0">\n' +
'</iframe>'
)
$("#" + containerId).html(iframe)
}
function loadVariantDetails(row, cell, show=false) {
var url = cell.data("url");
var icon = $("img", cell);
var previous_icon = "";
var current_icon = icon.attr("src");
if (current_icon === "/icons/fa-solid/chevron-right.svg") {
previous_icon = current_icon;
}
else if (current_icon === "/icons/fa-solid/chevron-down.svg") {
previous_icon = current_icon;
}
icon.attr("src", "/icons/fa-solid/spinner.svg");
icon.addClass("spin");
$.ajax(
url,
{
success: function (response) {
row.child(response);
icon.removeClass("spin");
if (show) {
icon.attr("src", "/icons/fa-solid/chevron-down.svg");
row.child.show();
}
else {
icon.attr("src", previous_icon);
}
$('[data-toggle="tooltip"]').tooltip({container: "body"});
$('[data-toggle="popover"]').popover({container: "body"});
var whitelist = $.fn.tooltip.Constructor.Default.whiteList
whitelist.iframe = ['src', 'style', 'width', 'height', 'frameborder', 'vspace', 'hspace']
// Alternative: skip sanitize function entirely
//$('[data-toggle="popover"]').popover({sanitizeFn: function(content) { return content }})
$('body').on('click', function (e) {
let element = $('.omim-popover');
// hide any open popovers when the anywhere else in the body is clicked
if (!element.is(e.target) && element.has(e.target).length === 0 && $('.popover').has(e.target).length === 0) {
element.popover('hide');
}
});
$(".comment-button-delete").on("click", commentDeleteToggle);
$(".comment-button-delete-cancel").on("click", commentDeleteToggle);
$(".comment-button-delete-submit").on("click", commentDeleteSubmit);
$(".comment-button-edit").on("click", commentEditToggle);
$(".comment-button-edit-cancel").on("click", commentEditToggle);
$(".comment-button-edit-submit").on("click", commentEditSubmit);
$(".link-load-beacon").on("click", loadBeaconWidget);
colorVariantEffects();
},
error: function (jqXHR, textStatus, errorThrown) {
alert("Error during AJAX call:", textStatus, + errorThrown);
console.log("Error during AJAX call: ", jqXHR, textStatus, errorThrown);
}
}
);
}
// we can't employ .click here because the html that it will work on is loaded afterwards.
$(document).on('click', '.toggle-variant-details', function() {
var row = dt.row($(this).parent());
var cell = $(this);
var icon = $("img", this);
// using toggleClass to shorten the code results in erroneous icon behaviour in border cases (e.g. fast opening/closing the details)
if (row.child.isShown()) {
icon.attr("src", "/icons/fa-solid/chevron-right.svg");
row.child.hide();
}
else {
if (row.child() && row.child().length) {
icon.attr("src", "/icons/fa-solid/chevron-down.svg");
row.child.show();
}
else {
loadVariantDetails(row, cell, true);
}
}
});
$("#settingsDownload").click(
function() {
var dump = $("#settingsDump").val();
$(this).attr('href', 'data:text/plain;charset=utf-8,' + encodeURIComponent(dump));
$(this).attr('download', 'settings_dump.json');
}
);
function activateClass(o) {
if (!$(o).hasClass("active")) {
$(o).addClass("active");
}
}
function updateSettings() {
var settings = JSON.parse($("#settingsDump").val());
var endings = ["_gt", "_dp_het", "_dp_hom", "_ad", "_gq", "_fail", "_ab"];
var failed = [];
for (var key in settings) {
for (var j = 0; j < endings.length; ++j) {
if (key.endsWith(endings[j]) && !$("#filterForm").find("input:not(:disabled)[name=" + key + "], select[name=" + key + "]").length) {
patient = key.slice(0, key.length - endings[j].length);
if (!failed.includes(patient)) {
failed.push(patient);
}
}
}
$("#filterForm").find("input:not(:disabled)[name=" + key + "], select[name=" + key + "], textarea[name=" + key + "]").each(
function(i) {
if ($(this).is(":radio")) {
label = "label[for='id_" + key + "_" + i + "']";
if ($(this).val() == settings[key]) {
activateClass(label);
$(this).prop("checked", true);
}
else {
$(this).prop("checked", false);
$(label).removeClass("active");
}
}
else if ($(this).is(":checkbox")) {
label = "label[for='id_" + key + "']";
if (settings[key]) {
activateClass(label);
}
else {
$(label).removeClass("active");
}
$(this).prop("checked", settings[key]);
}
else {
// also valid for select and textarea
$(this).val(settings[key]);
}
}
);
}
if (failed.length) {
alert("The following patients do not exist in pedigree: " + failed.join(", ") + ".\nPlease check your JSON input.");
}
}
function updateSettingsDump() {
var settings = {};
$("#filterForm").find("input, select, textarea").each(
function() {
if ($(this).attr("id") && $(this).attr("id").match("^template") || $(this).is(":disabled")) {
return;
}
if ($(this).is(":radio")) {
if ($(this).is(":checked")) {
settings[$(this).attr("name")] = $(this).val();
}
}
else if ($(this).is(":checkbox")) {
settings[$(this).attr("name")] = $(this).is(":checked");
}
else if ($(this).is("select")) {
settings[$(this).attr("name")] = $(this).find("option:selected").val();
}
else {
if ($(this).attr("name") == "settingsDump") {
return true;
}
settings[$(this).attr("name")] = $(this).val();
}
}
);
delete settings["csrfmiddlewaretoken"];
delete settings["undefined"];
delete settings["submit"];
$("#settingsDump").val(JSON.stringify(settings, null, 2));
if (structural_or_small === "small") {
updateQuickPresets(settings);
}
}
const presetsImpactNullVariant = {
"var_type_snv": true,
"var_type_mnv": true,
"var_type_indel": true,
"transcripts_coding": true,
"transcripts_noncoding": false,
"effect_complex_substitution": false,
"effect_direct_tandem_duplication": false,
"effect_disruptive_inframe_deletion": false,
"effect_disruptive_inframe_insertion": false,
"effect_exon_loss_variant": true,
"effect_feature_truncation": true,
"effect_frameshift_elongation": true,
"effect_frameshift_truncation": true,
"effect_frameshift_variant": true,
"effect_inframe_deletion": false,
"effect_inframe_insertion": false,
"effect_internal_feature_elongation": true,
"effect_start_lost": true,
"effect_stop_gained": true,
"effect_stop_lost": true,
"effect_structural_variant": true,
"effect_transcript_ablation": true,
"effect_splice_acceptor_variant": true,
"effect_splice_donor_variant": true,
"effect_missense_variant": false,
"effect_mnv": false,
"effect_splice_region_variant": false,
"effect_coding_transcript_intron_variant": false,
"effect_stop_retained_variant": true,
"effect_synonymous_variant": false,
"effect_five_prime_UTR_exon_variant": false,
"effect_five_prime_UTR_intron_variant": false,
"effect_three_prime_UTR_exon_variant": false,
"effect_three_prime_UTR_intron_variant": false,
"effect_downstream_gene_variant": false,
"effect_intergenic_variant": false,
"effect_non_coding_transcript_exon_variant": false,
"effect_non_coding_transcript_intron_variant": false,
"effect_upstream_gene_variant": false,
};
const presetsFlagsDefault = {
"flag_bookmarked": true,
"flag_candidate": true,
"flag_final_causative": true,
"flag_for_validation": true,
"flag_no_disease_association": true,
"flag_segregates": true,
"flag_doesnt_segregate": true,
"flag_simple_empty": true,
"flag_visual_positive": true,
"flag_visual_uncertain": true,
"flag_visual_negative": true,
"flag_visual_empty": true,
"flag_validation_positive": true,
"flag_validation_uncertain": true,
"flag_validation_negative": true,
"flag_validation_empty": true,
"flag_phenotype_match_positive": true,
"flag_phenotype_match_uncertain": true,
"flag_phenotype_match_negative": true,
"flag_phenotype_match_empty": true,
"flag_summary_positive": true,
"flag_summary_uncertain": true,
"flag_summary_negative": true,
"flag_summary_empty": true,
"require_in_hgmd_public": false,
"remove_if_in_dbsnp": false,
"require_in_clinvar": false,
"clinvar_include_benign": false,
"clinvar_include_likely_benign": false,
"clinvar_include_uncertain_significance": false,
"clinvar_include_likely_pathogenic": true,
"clinvar_include_pathogenic": true,
// "result_rows_limit": 200,
// "training_mode": false,
};
// Largest number of carriers/heterozygotes in in-house cohort to accept as "noise" or duplicated
// data sets.
const INHOUSE_MAX_NOISE = 20;
const presets = {
// Presets applied when using quick settings.
"quick-presets-auto": {
"ids": {
"file_type": "xlsx",
"result_rows_limit": 200,
"export_flags": true,
"export_comments": true,
},
"classes": {},
},
// Inheritance presets
"inheritance-any": {
"ids": {},
"classes": {"genotype-field-gt": "any"},
},
"inheritance-dominant": {
"ids": {},
// dom-denovo doesn't exist in the select. this triggers a function
"classes": {"genotype-field-gt": "dom-denovo"},
},
"inheritance-hom-recessive": {
"ids": {},
// hom-recessive doesn't exist in the select. this triggers a function
"classes": {"genotype-field-gt": "hom-recessive"},
},
"inheritance-comp-het": {
"ids": {},
"classes": {"genotype-field-gt": "index"},
},
"inheritance-recessive": {
"ids": {},
"classes": {"genotype-field-gt": "recessive-index"},
},
"inheritance-x-recessive": {
"ids": {},
"classes": {"genotype-field-gt": "x-recessive"},
},
"inheritance-mitochondrial": {
"ids": {},
// mitochondrial doesn't exist in the select. this triggers a function
"classes": {"genotype-field-gt": "mitochondrial"},
},
// Frequency presets
"frequency-super-strict": {
"ids": {
"thousand_genomes_enabled": true,
"thousand_genomes_homozygous": 0,
"thousand_genomes_heterozygous": 1,
"thousand_genomes_hemizygous": null,
"thousand_genomes_frequency": 0.002,
"exac_enabled": true,
"exac_homozygous": 0,
"exac_heterozygous": 1,
"exac_hemizygous": null,
"exac_frequency": 0.002,
"gnomad_exomes_enabled": true,
"gnomad_exomes_homozygous": 0,
"gnomad_exomes_heterozygous": 1,
"gnomad_exomes_hemizygous": null,
"gnomad_exomes_frequency": 0.002,
"gnomad_genomes_enabled": true,
"gnomad_genomes_homozygous": 0,
"gnomad_genomes_heterozygous": 1,
"gnomad_genomes_hemizygous": null,
"gnomad_genomes_frequency": 0.002,
"inhouse_enabled": true,
"inhouse_homozygous": null,
"inhouse_heterozygous": null,
"inhouse_hemizygous": null,
"inhouse_carriers": INHOUSE_MAX_NOISE,
"mtdb_enabled": false,
"mtdb_count": null,
"mtdb_frequency": null,
"helixmtdb_enabled": false,
"helixmtdb_het_count": null,
"helixmtdb_hom_count": null,
"helixmtdb_frequency": null,
"mitomap_enabled": false,
"mitomap_count": null,
"mitomap_frequency": null,
},
"classes": {},
},
"frequency-strict": {
"ids": {
"thousand_genomes_enabled": true,
"thousand_genomes_homozygous": 0,
"thousand_genomes_heterozygous": 4,
"thousand_genomes_hemizygous": null,
"thousand_genomes_frequency": 0.002,
"exac_enabled": true,
"exac_homozygous": 0,
"exac_heterozygous": 10,
"exac_hemizygous": null,
"exac_frequency": 0.002,
"gnomad_exomes_enabled": true,
"gnomad_exomes_homozygous": 0,
"gnomad_exomes_heterozygous": 20,
"gnomad_exomes_hemizygous": null,
"gnomad_exomes_frequency": 0.002,
"gnomad_genomes_enabled": true,
"gnomad_genomes_homozygous": 0,
"gnomad_genomes_heterozygous": 4,
"gnomad_genomes_hemizygous": null,
"gnomad_genomes_frequency": 0.002,
"inhouse_enabled": true,
"inhouse_homozygous": null,
"inhouse_heterozygous": null,
"inhouse_hemizygous": null,
"inhouse_carriers": INHOUSE_MAX_NOISE,
"mtdb_enabled": true,
"mtdb_count": 10,
"mtdb_frequency": 0.01,
"helixmtdb_enabled": true,
"helixmtdb_hom_count": 200,
"helixmtdb_het_count": null,
"helixmtdb_frequency": 0.01,
"mitomap_enabled": false,
"mitomap_count": null,
"mitomap_frequency": null,
},
"classes": {},
},
"frequency-relaxed": {
"ids": {
"thousand_genomes_enabled": true,
"thousand_genomes_homozygous": 0,
"thousand_genomes_heterozygous": 10,
"thousand_genomes_hemizygous": null,
"thousand_genomes_frequency": 0.01,
"exac_enabled": true,
"exac_homozygous": 0,
"exac_heterozygous": 25,
"exac_hemizygous": null,
"exac_frequency": 0.01,
"gnomad_exomes_enabled": true,
"gnomad_exomes_homozygous": 0,
"gnomad_exomes_heterozygous": 50,
"gnomad_exomes_hemizygous": null,
"gnomad_exomes_frequency": 0.01,
"gnomad_genomes_enabled": true,
"gnomad_genomes_homozygous": 0,
"gnomad_genomes_heterozygous": 20,
"gnomad_genomes_hemizygous": null,
"gnomad_genomes_frequency": 0.01,
"inhouse_enabled": true,
"inhouse_homozygous": null,
"inhouse_heterozygous": null,
"inhouse_hemizygous": null,
"inhouse_carriers": INHOUSE_MAX_NOISE,
"mtdb_enabled": true,
"mtdb_count": 50,
"mtdb_frequency": 0.15,
"helixmtdb_enabled": true,
"helixmtdb_het_count": null,
"helixmtdb_hom_count": 400,
"helixmtdb_frequency": 0.15,
"mitomap_enabled": false,
"mitomap_count": null,
"mitomap_frequency": null,
},
"classes": {},
},
"frequency-recessive-strict": {
"ids": {
"thousand_genomes_enabled": true,
"thousand_genomes_homozygous": 0,
"thousand_genomes_heterozygous": 24,
"thousand_genomes_hemizygous": null,
"thousand_genomes_frequency": 0.001,
"exac_enabled": true,
"exac_homozygous": 0,
"exac_heterozygous": 60,
"exac_hemizygous": null,
"exac_frequency": 0.001,
"gnomad_exomes_enabled": true,
"gnomad_exomes_homozygous": 0,
"gnomad_exomes_heterozygous": 120,
"gnomad_exomes_hemizygous": null,
"gnomad_exomes_frequency": 0.001,
"gnomad_genomes_enabled": true,
"gnomad_genomes_homozygous": 0,
"gnomad_genomes_heterozygous": 15,
"gnomad_genomes_hemizygous": null,
"gnomad_genomes_frequency": 0.001,
"inhouse_enabled": true,
"inhouse_homozygous": null,
"inhouse_heterozygous": null,
"inhouse_hemizygous": null,
"inhouse_carriers": INHOUSE_MAX_NOISE,
"mtdb_enabled": false,
"mtdb_count": null,
"mtdb_frequency": null,
"helixmtdb_enabled": false,
"helixmtdb_het_count": null,
"helixmtdb_hom_count": null,
"helixmtdb_frequency": null,
"mitomap_enabled": false,
"mitomap_count": null,
"mitomap_frequency": null,
},
"classes": {},
},
"frequency-recessive-relaxed": {
"ids": {
"thousand_genomes_enabled": true,
"thousand_genomes_homozygous": 4,
"thousand_genomes_heterozygous": 240,
"thousand_genomes_hemizygous": null,
"thousand_genomes_frequency": 0.01,
"exac_enabled": true,
"exac_homozygous": 10,
"exac_heterozygous": 600,
"exac_hemizygous": null,
"exac_frequency": 0.01,
"gnomad_exomes_enabled": true,
"gnomad_exomes_homozygous": 20,
"gnomad_exomes_heterozygous": 1200,
"gnomad_exomes_hemizygous": null,
"gnomad_exomes_frequency": 0.01,
"gnomad_genomes_enabled": true,
"gnomad_genomes_homozygous": 4,
"gnomad_genomes_heterozygous": 150,
"gnomad_genomes_hemizygous": null,
"gnomad_genomes_frequency": 0.01,
"inhouse_enabled": true,
"inhouse_homozygous": null,
"inhouse_heterozygous": null,
"inhouse_hemizygous": null,
"inhouse_carriers": INHOUSE_MAX_NOISE,
"mtdb_enabled": false,
"mtdb_count": null,
"mtdb_frequency": null,
"helixmtdb_enabled": false,
"helixmtdb_het_count": null,
"helixmtdb_hom_count": null,
"helixmtdb_frequency": null,
"mitomap_enabled": false,
"mitomap_count": null,
"mitomap_frequency": null,
},
"classes": {},
},
"frequency-all": {
"ids": {
"thousand_genomes_enabled": false,
"thousand_genomes_homozygous": null,
"thousand_genomes_heterozygous": null,
"thousand_genomes_hemizygous": null,
"thousand_genomes_frequency": null,
"exac_enabled": false,
"exac_homozygous": null,
"exac_heterozygous": null,
"exac_hemizygous": null,
"exac_frequency": null,
"gnomad_exomes_enabled": false,
"gnomad_exomes_homozygous": null,
"gnomad_exomes_heterozygous": null,
"gnomad_exomes_hemizygous": null,
"gnomad_exomes_frequency": null,
"gnomad_genomes_enabled": false,
"gnomad_genomes_homozygous": null,
"gnomad_genomes_heterozygous": null,
"gnomad_genomes_hemizygous": null,
"gnomad_genomes_frequency": null,
"inhouse_enabled": false,
"inhouse_homozygous": null,
"inhouse_heterozygous": null,
"inhouse_carriers": null,
"mtdb_enabled": false,
"mtdb_count": null,
"mtdb_frequency": null,
"helixmtdb_enabled": false,
"helixmtdb_het_count": null,
"helixmtdb_hom_count": null,
"helixmtdb_frequency": null,
"mitomap_enabled": false,
"mitomap_count": null,
"mitomap_frequency": null,
},
"classes": {},
},
// Impact presets
"impact-null-variant": {
"ids": presetsImpactNullVariant,
"classes": {},
},
"impact-aa-change": {
"ids": Object.assign({}, presetsImpactNullVariant , {
"effect_complex_substitution": true,
"effect_direct_tandem_duplication": true,
"effect_disruptive_inframe_deletion": true,
"effect_disruptive_inframe_insertion": true,
"effect_inframe_deletion": true,
"effect_inframe_insertion": true,
"effect_missense_variant": true,
"effect_mnv": true,
"effect_splice_region_variant": true,
}),
"classes": {},
},
"impact-all-coding-deep-intronic": {
"ids": Object.assign({}, presetsImpactNullVariant , {
"effect_complex_substitution": true,
"effect_direct_tandem_duplication": true,
"effect_disruptive_inframe_deletion": true,
"effect_disruptive_inframe_insertion": true,
"effect_inframe_deletion": true,
"effect_inframe_insertion": true,
"effect_missense_variant": true,
"effect_mnv": true,
"effect_splice_region_variant": true,
"effect_synonymous_variant": true,
"effect_coding_transcript_intron_variant": true,
}),
"classes": {},
},
"impact-whole-transcript": {
"ids": Object.assign({}, presetsImpactNullVariant , {
"effect_complex_substitution": true,
"effect_direct_tandem_duplication": true,
"effect_disruptive_inframe_deletion": true,
"effect_disruptive_inframe_insertion": true,
"effect_inframe_deletion": true,
"effect_inframe_insertion": true,
"effect_missense_variant": true,
"effect_mnv": true,
"effect_splice_region_variant": true,
"effect_coding_transcript_intron_variant": true,
"effect_stop_retained_variant": true,
"effect_synonymous_variant": true,
"effect_five_prime_UTR_exon_variant": true,
"effect_five_prime_UTR_intron_variant": true,
"effect_three_prime_UTR_exon_variant": true,
"effect_three_prime_UTR_intron_variant": true,
}),
"classes": {},
},
"impact-any": {
"ids": Object.assign({}, presetsImpactNullVariant , {
"effect_complex_substitution": true,
"effect_direct_tandem_duplication": true,
"effect_disruptive_inframe_deletion": true,
"effect_disruptive_inframe_insertion": true,
"effect_inframe_deletion": true,
"effect_inframe_insertion": true,
"effect_missense_variant": true,
"effect_mnv": true,
"effect_splice_region_variant": true,
"effect_coding_transcript_intron_variant": true,
"effect_stop_retained_variant": true,
"effect_synonymous_variant": true,
"effect_five_prime_UTR_exon_variant": true,
"effect_five_prime_UTR_intron_variant": true,
"effect_three_prime_UTR_exon_variant": true,
"effect_three_prime_UTR_intron_variant": true,
"transcripts_noncoding": true,
"effect_downstream_gene_variant": true,
"effect_intergenic_variant": true,
"effect_non_coding_transcript_exon_variant": true,
"effect_non_coding_transcript_intron_variant": true,
"effect_upstream_gene_variant": true,
}),
"classes": {},
},
// Quality presets
"quality-super-strict": {
"ids": {},
"classes": {
"quality-field-dp-het": 10,
"quality-field-dp-hom": 5,
"quality-field-ab": 0.3,
"quality-field-gq": 30,
"quality-field-ad": 3,
"quality-field-fail": "drop-variant",
"quality-field-ad-max": null,
},
},
"quality-strict": {
"ids": {},
"classes": {
"quality-field-dp-het": 10,
"quality-field-dp-hom": 5,
"quality-field-ab": 0.2,
"quality-field-gq": 10,
"quality-field-ad": 3,
"quality-field-fail": "drop-variant",
"quality-field-ad-max": null,
},
},
"quality-relaxed": {
"ids": {},
"classes": {
"quality-field-dp-het": 8,
"quality-field-dp-hom": 4,
"quality-field-ab": 0.1,
"quality-field-gq": 10,
"quality-field-ad": 2,
"quality-field-fail": "drop-variant",
"quality-field-ad-max": null,
},
},
"quality-ignore": {
"ids": {},
"classes": {
"quality-field-dp-het": 0,
"quality-field-dp-hom": 0,
"quality-field-ab": 0.0,
"quality-field-gq": 0,
"quality-field-ad": 0,
"quality-field-fail": "ignore",
"quality-field-ad-max": null,
},
},
// Region presets
"region-whole-genome": {
"ids": {
"gene_blocklist": "",
"gene_allowlist": "",
"genomic_region": "",
},
"classes": {},
},
"region-autosomes": {
"ids": {
"gene_blocklist": "",
"gene_allowlist": "",
"genomic_region": "chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 " +
"chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22",
},
"classes": {},
},
"region-x-chromosome": {
"ids": {
"gene_blocklist": "",
"gene_allowlist": "",
"genomic_region": "chrX",
},
"classes": {},
},
"region-y-chromosome": {
"ids": {
"gene_blocklist": "",
"gene_allowlist": "",
"genomic_region": "chrY",
},
"classes": {},
},
"region-mt-chromosome": {
"ids": {
"gene_blocklist": "",
"gene_allowlist": "",
"genomic_region": "chrMT",
},
"classes": {},
},
"region-clinvar": {
"ids": {
"gene_blocklist": "",
"gene_allowlist": "",
"genomic_region": "",
},
"classes": {},
},
// flags etc.
"flags-default": {