presentation_241030_necker/Images/first_pass_flow.svg

<svg id="mermaid-svg" width="100%" xmlns="http://www.w3.org/2000/svg" style="max-width: 541.84765625px;" viewBox="-8 -8 541.84765625 1073.546875" role="graphics-document document" aria-roledescription="flowchart-v2" xmlns:xlink="http://www.w3.org/1999/xlink"><style>#mermaid-svg{font-family:"trebuchet ms",verdana,arial,sans-serif;font-size:16px;fill:#333;}#mermaid-svg .error-icon{fill:#552222;}#mermaid-svg .error-text{fill:#552222;stroke:#552222;}#mermaid-svg .edge-thickness-normal{stroke-width:2px;}#mermaid-svg .edge-thickness-thick{stroke-width:3.5px;}#mermaid-svg .edge-pattern-solid{stroke-dasharray:0;}#mermaid-svg .edge-pattern-dashed{stroke-dasharray:3;}#mermaid-svg .edge-pattern-dotted{stroke-dasharray:2;}#mermaid-svg .marker{fill:#333333;stroke:#333333;}#mermaid-svg .marker.cross{stroke:#333333;}#mermaid-svg svg{font-family:"trebuchet ms",verdana,arial,sans-serif;font-size:16px;}#mermaid-svg .label{font-family:"trebuchet ms",verdana,arial,sans-serif;color:#333;}#mermaid-svg .cluster-label text{fill:#333;}#mermaid-svg .cluster-label span,#mermaid-svg p{color:#333;}#mermaid-svg .label text,#mermaid-svg span,#mermaid-svg p{fill:#333;color:#333;}#mermaid-svg .node rect,#mermaid-svg .node circle,#mermaid-svg .node ellipse,#mermaid-svg .node polygon,#mermaid-svg .node path{fill:#ECECFF;stroke:#9370DB;stroke-width:1px;}#mermaid-svg .flowchart-label text{text-anchor:middle;}#mermaid-svg .node .label{text-align:center;}#mermaid-svg .node.clickable{cursor:pointer;}#mermaid-svg .arrowheadPath{fill:#333333;}#mermaid-svg .edgePath .path{stroke:#333333;stroke-width:2.0px;}#mermaid-svg .flowchart-link{stroke:#333333;fill:none;}#mermaid-svg .edgeLabel{background-color:#e8e8e8;text-align:center;}#mermaid-svg .edgeLabel rect{opacity:0.5;background-color:#e8e8e8;fill:#e8e8e8;}#mermaid-svg .labelBkg{background-color:rgba(232, 232, 232, 0.5);}#mermaid-svg .cluster rect{fill:#ffffde;stroke:#aaaa33;stroke-width:1px;}#mermaid-svg .cluster text{fill:#333;}#mermaid-svg .cluster span,#mermaid-svg p{color:#333;}#mermaid-svg div.mermaidTooltip{position:absolute;text-align:center;max-width:200px;padding:2px;font-family:"trebuchet ms",verdana,arial,sans-serif;font-size:12px;background:hsl(80, 100%, 96.2745098039%);border:1px solid #aaaa33;border-radius:2px;pointer-events:none;z-index:100;}#mermaid-svg .flowchartTitleText{text-anchor:middle;font-size:18px;fill:#333;}#mermaid-svg :root{--mermaid-font-family:"trebuchet ms",verdana,arial,sans-serif;}</style><g><marker id="mermaid-svg_flowchart-pointEnd" class="marker flowchart" viewBox="0 0 10 10" refX="6" refY="5" markerUnits="userSpaceOnUse" markerWidth="12" markerHeight="12" orient="auto"><path d="M 0 0 L 10 5 L 0 10 z" class="arrowMarkerPath" style="stroke-width: 1; stroke-dasharray: 1, 0;"></path></marker><marker id="mermaid-svg_flowchart-pointStart" class="marker flowchart" viewBox="0 0 10 10" refX="4.5" refY="5" markerUnits="userSpaceOnUse" markerWidth="12" markerHeight="12" orient="auto"><path d="M 0 5 L 10 10 L 10 0 z" class="arrowMarkerPath" style="stroke-width: 1; stroke-dasharray: 1, 0;"></path></marker><marker id="mermaid-svg_flowchart-circleEnd" class="marker flowchart" viewBox="0 0 10 10" refX="11" refY="5" markerUnits="userSpaceOnUse" markerWidth="11" markerHeight="11" orient="auto"><circle cx="5" cy="5" r="5" class="arrowMarkerPath" style="stroke-width: 1; stroke-dasharray: 1, 0;"></circle></marker><marker id="mermaid-svg_flowchart-circleStart" class="marker flowchart" viewBox="0 0 10 10" refX="-1" refY="5" markerUnits="userSpaceOnUse" markerWidth="11" markerHeight="11" orient="auto"><circle cx="5" cy="5" r="5" class="arrowMarkerPath" style="stroke-width: 1; stroke-dasharray: 1, 0;"></circle></marker><marker id="mermaid-svg_flowchart-crossEnd" class="marker cross flowchart" viewBox="0 0 11 11" refX="12" refY="5.2" markerUnits="userSpaceOnUse" markerWidth="11" markerHeight="11" orient="auto"><path d="M 1,1 l 9,9 M 10,1 l -9,9" class="arrowMarkerPath" style="stroke-width: 2; stroke-dasharray: 1, 0;"></path></marker><marker id="mermaid-svg_flowchart-crossStart" class="marker cross flowchart" viewBox="0 0 11 11" refX="-1" refY="5.2" markerUnits="userSpaceOnUse" markerWidth="11" markerHeight="11" orient="auto"><path d="M 1,1 l 9,9 M 10,1 l -9,9" class="arrowMarkerPath" style="stroke-width: 2; stroke-dasharray: 1, 0;"></path></marker><g class="root"><g class="clusters"></g><g class="edgePaths"><path d="M127.145,34L127.145,38.167C127.145,42.333,127.145,50.667,127.145,58.117C127.145,65.567,127.145,72.133,127.145,75.417L127.145,78.7" id="L-Z-ZZ-0" class=" edge-thickness-normal edge-pattern-solid flowchart-link LS-Z LE-ZZ" style="fill:none;" marker-end="url(#mermaid-svg_flowchart-pointEnd)"></path><path d="M127.145,118L127.145,123.75C127.145,129.5,127.145,141,140.567,160.127C153.989,179.254,180.834,206.009,194.256,219.386L207.679,232.763" id="L-ZZ-B-0" class=" edge-thickness-normal edge-pattern-solid flowchart-link LS-ZZ LE-B" style="fill:none;" marker-end="url(#mermaid-svg_flowchart-pointEnd)"></path><path d="M392.73,118L392.73,123.75C392.73,129.5,392.73,141,379.471,160.124C366.212,179.247,339.693,205.994,326.433,219.368L313.174,232.741" id="L-A-B-0" class=" edge-thickness-normal edge-pattern-solid flowchart-link LS-A LE-B" style="fill:none;" marker-end="url(#mermaid-svg_flowchart-pointEnd)"></path><path d="M216.383,339.133L205.577,352.142C194.771,365.151,173.159,391.169,162.424,409.129C151.688,427.088,151.83,436.988,151.9,441.938L151.971,446.888" id="L-B-C-0" class=" edge-thickness-normal edge-pattern-solid flowchart-link LS-B LE-C" style="fill:none;" marker-end="url(#mermaid-svg_flowchart-pointEnd)"></path><path d="M304.492,339.133L315.131,352.142C325.77,365.151,347.049,391.169,357.689,420.588C368.328,450.007,368.328,482.826,368.328,499.236L368.328,515.645" id="L-B-I-0" class=" edge-thickness-normal edge-pattern-solid flowchart-link LS-B LE-I" style="fill:none;" marker-end="url(#mermaid-svg_flowchart-pointEnd)"></path><path d="M117.773,590.429L110.133,601.808C102.492,613.187,87.211,635.945,79.57,655.575C71.93,675.205,71.93,691.706,71.93,699.957L71.93,708.208" id="L-C-D-0" class=" edge-thickness-normal edge-pattern-solid flowchart-link LS-C LE-D" style="fill:none;" marker-end="url(#mermaid-svg_flowchart-pointEnd)"></path><path d="M186.321,590.429L193.795,601.808C201.268,613.187,216.216,635.945,223.761,652.274C231.305,668.603,231.447,678.503,231.518,683.454L231.588,688.404" id="L-C-E-0" class=" edge-thickness-normal edge-pattern-solid flowchart-link LS-C LE-E" style="fill:none;" marker-end="url(#mermaid-svg_flowchart-pointEnd)"></path><path d="M212.983,749.632L205.597,756.828C198.211,764.025,183.44,778.419,176.054,801.177C168.668,823.935,168.668,855.057,168.668,887.763C168.668,920.469,168.668,954.758,169.616,976.785C170.564,998.813,172.46,1008.578,173.409,1013.461L174.357,1018.344" id="L-E-F-0" class=" edge-thickness-normal edge-pattern-solid flowchart-link LS-E LE-F" style="fill:none;" marker-end="url(#mermaid-svg_flowchart-pointEnd)"></path><path d="M250.024,749.953L256.944,757.096C263.863,764.239,277.703,778.526,284.689,789.036C291.675,799.546,291.807,806.28,291.873,809.647L291.939,813.014" id="L-E-G-0" class=" edge-thickness-normal edge-pattern-solid flowchart-link LS-E LE-G" style="fill:none;" marker-end="url(#mermaid-svg_flowchart-pointEnd)"></path><path d="M303.664,943.426L305.155,951.029C306.646,958.633,309.628,973.84,311.118,986.31C312.609,998.78,312.609,1008.514,312.609,1013.38L312.609,1018.247" id="L-G-H-0" class=" edge-thickness-normal edge-pattern-solid flowchart-link LS-G LE-H" style="fill:none;" marker-end="url(#mermaid-svg_flowchart-pointEnd)"></path><path d="M268.942,931.946L263.96,941.463C258.977,950.98,249.012,970.013,237.96,984.707C226.908,999.4,214.77,1009.754,208.701,1014.931L202.631,1020.107" id="L-G-F-0" class=" edge-thickness-normal edge-pattern-solid flowchart-link LS-G LE-F" style="fill:none;" marker-end="url(#mermaid-svg_flowchart-pointEnd)"></path></g><g class="edgeLabels"><g class="edgeLabel"><g class="label" transform="translate(0, 0)"><foreignObject width="0" height="0"><div xmlns="http://www.w3.org/1999/xhtml" style="display: inline-block; white-space: nowrap;"><span class="edgeLabel"></span></div></foreignObject></g></g><g class="edgeLabel"><g class="label" transform="translate(0, 0)"><foreignObject width="0" height="0"><div xmlns="http://www.w3.org/1999/xhtml" style="display: inline-block; white-space: nowrap;"><span class="edgeLabel"></span></div></foreignObject></g></g><g class="edgeLabel" transform="translate(392.73046875, 152.5)"><g class="label" transform="translate(-33.546875, -9.5)"><foreignObject width="67.09375" height="19"><div xmlns="http://www.w3.org/1999/xhtml" style="display: inline-block; white-space: nowrap;"><span class="edgeLabel">First pass</span></div></foreignObject></g></g><g class="edgeLabel" transform="translate(151.546875, 417.1875)"><g class="label" transform="translate(-11.546875, -9.5)"><foreignObject width="23.09375" height="19"><div xmlns="http://www.w3.org/1999/xhtml" style="display: inline-block; white-space: nowrap;"><span class="edgeLabel">yes</span></div></foreignObject></g></g><g class="edgeLabel" transform="translate(368.328125, 417.1875)"><g class="label" transform="translate(-8.6640625, -9.5)"><foreignObject width="17.328125" height="19"><div xmlns="http://www.w3.org/1999/xhtml" style="display: inline-block; white-space: nowrap;"><span class="edgeLabel">no</span></div></foreignObject></g></g><g class="edgeLabel" transform="translate(71.9296875, 658.703125)"><g class="label" transform="translate(-11.546875, -9.5)"><foreignObject width="23.09375" height="19"><div xmlns="http://www.w3.org/1999/xhtml" style="display: inline-block; white-space: nowrap;"><span class="edgeLabel">yes</span></div></foreignObject></g></g><g class="edgeLabel" transform="translate(231.1640625, 658.703125)"><g class="label" transform="translate(-8.6640625, -9.5)"><foreignObject width="17.328125" height="19"><div xmlns="http://www.w3.org/1999/xhtml" style="display: inline-block; white-space: nowrap;"><span class="edgeLabel">no</span></div></foreignObject></g></g><g class="edgeLabel" transform="translate(168.66796875, 886.1796875)"><g class="label" transform="translate(-17.390625, -9.5)"><foreignObject width="34.78125" height="19"><div xmlns="http://www.w3.org/1999/xhtml" style="display: inline-block; white-space: nowrap;"><span class="edgeLabel">100%</span></div></foreignObject></g></g><g class="edgeLabel"><g class="label" transform="translate(0, 0)"><foreignObject width="0" height="0"><div xmlns="http://www.w3.org/1999/xhtml" style="display: inline-block; white-space: nowrap;"><span class="edgeLabel"></span></div></foreignObject></g></g><g class="edgeLabel" transform="translate(312.609375, 989.046875)"><g class="label" transform="translate(-22.1328125, -9.5)"><foreignObject width="44.265625" height="19"><div xmlns="http://www.w3.org/1999/xhtml" style="display: inline-block; white-space: nowrap;"><span class="edgeLabel">&lt; 0.01</span></div></foreignObject></g></g><g class="edgeLabel"><g class="label" transform="translate(0, 0)"><foreignObject width="0" height="0"><div xmlns="http://www.w3.org/1999/xhtml" style="display: inline-block; white-space: nowrap;"><span class="edgeLabel"></span></div></foreignObject></g></g></g><g class="nodes"><g class="node default default flowchart-label" id="flowchart-Z-0" transform="translate(127.14453125, 17)"><rect class="basic label-container" style="" rx="0" ry="0" x="-104.7265625" y="-17" width="209.453125" height="34"></rect><g class="label" style="" transform="translate(-97.2265625, -9.5)"><rect></rect><foreignObject width="194.453125" height="19"><div xmlns="http://www.w3.org/1999/xhtml" style="display: inline-block; white-space: nowrap;"><span class="nodeLabel">Variants from VCFs constit:</span></div></foreignObject></g></g><g class="node default default flowchart-label" id="flowchart-ZZ-1" transform="translate(127.14453125, 101)"><rect class="basic label-container" style="" rx="0" ry="0" x="-82.46875" y="-17" width="164.9375" height="34"></rect><g class="label" style="" transform="translate(-74.96875, -9.5)"><rect></rect><foreignObject width="149.9375" height="19"><div xmlns="http://www.w3.org/1999/xhtml" style="display: inline-block; white-space: nowrap;"><span class="nodeLabel">Into constit registery</span></div></foreignObject></g></g><g class="node default default flowchart-label" id="flowchart-B-2" transform="translate(259.9375, 284.84375)"><polygon points="97.84375,0 195.6875,-97.84375 97.84375,-195.6875 0,-97.84375" class="label-container" transform="translate(-97.84375,97.84375)" style=""></polygon><g class="label" style="" transform="translate(-63.84375, -19)"><rect></rect><foreignObject width="127.6875" height="38"><div xmlns="http://www.w3.org/1999/xhtml" style="display: inline-block; white-space: nowrap;"><span class="nodeLabel">Variant is in <br/>    constit registery ?</span></div></foreignObject></g></g><g class="node default default flowchart-label" id="flowchart-A-3" transform="translate(392.73046875, 101)"><rect class="basic label-container" style="" rx="0" ry="0" x="-133.1171875" y="-17" width="266.234375" height="34"></rect><g class="label" style="" transform="translate(-125.6171875, -9.5)"><rect></rect><foreignObject width="251.234375" height="19"><div xmlns="http://www.w3.org/1999/xhtml" style="display: inline-block; white-space: nowrap;"><span class="nodeLabel">Variants from VCFs bulk: 4,458,549</span></div></foreignObject></g></g><g class="node default default flowchart-label" id="flowchart-C-6" transform="translate(151.546875, 537.9453125)"><polygon points="86.2578125,0 172.515625,-86.2578125 86.2578125,-172.515625 0,-86.2578125" class="label-container" transform="translate(-86.2578125,86.2578125)" style=""></polygon><g class="label" style="" transform="translate(-61.7578125, -9.5)"><rect></rect><foreignObject width="123.515625" height="19"><div xmlns="http://www.w3.org/1999/xhtml" style="display: inline-block; white-space: nowrap;"><span class="nodeLabel">Constit depth &lt; 6</span></div></foreignObject></g></g><g class="node default default flowchart-label" id="flowchart-I-8" transform="translate(368.328125, 537.9453125)"><rect class="basic label-container" style="" rx="0" ry="0" x="-80.5234375" y="-17" width="161.046875" height="34"></rect><g class="label" style="" transform="translate(-73.0234375, -9.5)"><rect></rect><foreignObject width="146.046875" height="19"><div xmlns="http://www.w3.org/1999/xhtml" style="display: inline-block; white-space: nowrap;"><span class="nodeLabel">Into the second pass</span></div></foreignObject></g></g><g class="node default default flowchart-label" id="flowchart-D-10" transform="translate(71.9296875, 730.5078125)"><rect class="basic label-container" style="" rx="0" ry="0" x="-71.9296875" y="-17" width="143.859375" height="34"></rect><g class="label" style="" transform="translate(-64.4296875, -9.5)"><rect></rect><foreignObject width="128.859375" height="19"><div xmlns="http://www.w3.org/1999/xhtml" style="display: inline-block; white-space: nowrap;"><span class="nodeLabel">Low constit depth</span></div></foreignObject></g></g><g class="node default default flowchart-label" id="flowchart-E-12" transform="translate(231.1640625, 730.5078125)"><polygon points="37.3046875,0 74.609375,-37.3046875 37.3046875,-74.609375 0,-37.3046875" class="label-container" transform="translate(-37.3046875,37.3046875)" style=""></polygon><g class="label" style="" transform="translate(-12.8046875, -9.5)"><rect></rect><foreignObject width="25.609375" height="19"><div xmlns="http://www.w3.org/1999/xhtml" style="display: inline-block; white-space: nowrap;"><span class="nodeLabel">VAF</span></div></foreignObject></g></g><g class="node default default flowchart-label" id="flowchart-F-14" transform="translate(178.66796875, 1040.546875)"><rect class="basic label-container" style="" rx="0" ry="0" x="-32.8125" y="-17" width="65.625" height="34"></rect><g class="label" style="" transform="translate(-25.3125, -9.5)"><rect></rect><foreignObject width="50.625" height="19"><div xmlns="http://www.w3.org/1999/xhtml" style="display: inline-block; white-space: nowrap;"><span class="nodeLabel">Constit</span></div></foreignObject></g></g><g class="node default default flowchart-label" id="flowchart-G-16" transform="translate(291.54296875, 886.1796875)"><polygon points="68.3671875,0 136.734375,-68.3671875 68.3671875,-136.734375 0,-68.3671875" class="label-container" transform="translate(-68.3671875,68.3671875)" style=""></polygon><g class="label" style="" transform="translate(-43.8671875, -9.5)"><rect></rect><foreignObject width="87.734375" height="19"><div xmlns="http://www.w3.org/1999/xhtml" style="display: inline-block; white-space: nowrap;"><span class="nodeLabel">Chi2 AF pval</span></div></foreignObject></g></g><g class="node default default flowchart-label" id="flowchart-H-18" transform="translate(312.609375, 1040.546875)"><rect class="basic label-container" style="" rx="0" ry="0" x="-22.1796875" y="-17" width="44.359375" height="34"></rect><g class="label" style="" transform="translate(-14.6796875, -9.5)"><rect></rect><foreignObject width="29.359375" height="19"><div xmlns="http://www.w3.org/1999/xhtml" style="display: inline-block; white-space: nowrap;"><span class="nodeLabel">LOH</span></div></foreignObject></g></g></g></g></g><style>@import url("https://cdnjs.cloudflare.com/ajax/libs/font-awesome/6.4.0/css/all.min.css");</style></svg>