docs/call-gSV.svg

<?xml version="1.0" encoding="UTF-8" standalone="no"?><svg xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink" contentStyleType="text/css" height="835px" preserveAspectRatio="none" style="width:1159px;height:835px;background:#FFFFFF;" version="1.1" viewBox="0 0 1159 835" width="1159px" zoomAndPan="magnify"><defs/><g><ellipse cx="576.5" cy="20" fill="#222222" rx="10" ry="10" style="stroke:#222222;stroke-width:1.0;"/><rect fill="#F1F1F1" height="64.2344" rx="12.5" ry="12.5" style="stroke:#181818;stroke-width:0.5;" width="130" x="511.5" y="50"/><text fill="#000000" font-family="sans-serif" font-size="14" font-weight="bold" lengthAdjust="spacing" textLength="94" x="521.5" y="72.9951">Normal BAM</text><text fill="#000000" font-family="sans-serif" font-size="12" lengthAdjust="spacing" textLength="12" x="521.5" y="87.4355">---</text><text fill="#000000" font-family="sans-serif" font-size="12" lengthAdjust="spacing" textLength="110" x="521.5" y="101.4043">Input Normal BAM</text><rect fill="#F1F1F1" height="64.2344" rx="12.5" ry="12.5" style="stroke:#181818;stroke-width:0.5;" width="344" x="404.5" y="134.2344"/><text fill="#000000" font-family="sans-serif" font-size="14" font-weight="bold" lengthAdjust="spacing" textLength="122" x="414.5" y="157.2295">Input Validation</text><text fill="#000000" font-family="sans-serif" font-size="12" lengthAdjust="spacing" textLength="12" x="414.5" y="171.6699">---</text><text fill="#000000" font-family="sans-serif" font-size="12" lengthAdjust="spacing" textLength="324" x="414.5" y="185.6387">Validate the input BAM and corresponding index file</text><rect fill="#555555" height="6" rx="2.5" ry="2.5" style="stroke:#555555;stroke-width:1.0;" width="1137" x="11" y="218.4688"/><line style="stroke:#181818;stroke-width:1.5;" x1="130" x2="369" y1="292.8711" y2="292.8711"/><rect fill="#F1F1F1" height="78.2031" rx="12.5" ry="12.5" style="stroke:#181818;stroke-width:0.5;" width="205" x="27.5" y="312.8711"/><text fill="#000000" font-family="sans-serif" font-size="14" font-weight="bold" lengthAdjust="spacing" textLength="84" x="37.5" y="335.8662">DELLY gSV</text><text fill="#000000" font-family="sans-serif" font-size="12" lengthAdjust="spacing" textLength="12" x="37.5" y="350.3066">---</text><text fill="#000000" font-family="sans-serif" font-size="12" lengthAdjust="spacing" textLength="185" x="37.5" y="364.2754">Call germline SVs using DELLY</text><text fill="#000000" font-family="sans-serif" font-size="12" lengthAdjust="spacing" textLength="33" x="37.5" y="378.2441">(BCF)</text><rect fill="#F1F1F1" height="78.2031" rx="12.5" ry="12.5" style="stroke:#181818;stroke-width:0.5;" width="214" x="23" y="426.0742"/><text fill="#000000" font-family="sans-serif" font-size="14" font-weight="bold" lengthAdjust="spacing" textLength="96" x="33" y="449.0693">DELLY gCNV</text><text fill="#000000" font-family="sans-serif" font-size="12" lengthAdjust="spacing" textLength="12" x="33" y="463.5098">---</text><text fill="#000000" font-family="sans-serif" font-size="12" lengthAdjust="spacing" textLength="194" x="33" y="477.4785">Call germline CNVs using DELLY</text><text fill="#000000" font-family="sans-serif" font-size="12" lengthAdjust="spacing" textLength="33" x="33" y="491.4473">(BCF)</text><rect fill="#F1F1F1" height="64.2344" rx="12.5" ry="12.5" style="stroke:#181818;stroke-width:0.5;" width="183" x="38.5" y="539.2773"/><text fill="#000000" font-family="sans-serif" font-size="14" font-weight="bold" lengthAdjust="spacing" textLength="23" x="48.5" y="562.2725">QC</text><text fill="#000000" font-family="sans-serif" font-size="12" lengthAdjust="spacing" textLength="12" x="48.5" y="576.7129">---</text><text fill="#000000" font-family="sans-serif" font-size="12" lengthAdjust="spacing" textLength="163" x="48.5" y="590.6816">Quality Check variant calls</text><rect fill="#F1F1F1" height="64.2344" rx="12.5" ry="12.5" style="stroke:#181818;stroke-width:0.5;" width="156" x="52" y="638.5117"/><text fill="#000000" font-family="sans-serif" font-size="14" font-weight="bold" lengthAdjust="spacing" textLength="136" x="62" y="661.5068">Output Validation</text><text fill="#000000" font-family="sans-serif" font-size="12" lengthAdjust="spacing" textLength="12" x="62" y="675.9473">---</text><text fill="#000000" font-family="sans-serif" font-size="12" lengthAdjust="spacing" textLength="124" x="62" y="689.916">Validate BCF output</text><rect fill="#F1F1F1" height="78.2031" rx="12.5" ry="12.5" style="stroke:#181818;stroke-width:0.5;" width="208" x="265" y="468.707"/><text fill="#000000" font-family="sans-serif" font-size="14" font-weight="bold" lengthAdjust="spacing" textLength="83" x="275" y="491.7021">Manta gSV</text><text fill="#000000" font-family="sans-serif" font-size="12" lengthAdjust="spacing" textLength="12" x="275" y="506.1426">---</text><text fill="#000000" font-family="sans-serif" font-size="12" lengthAdjust="spacing" textLength="188" x="275" y="520.1113">Call germline SVs using Manta</text><text fill="#000000" font-family="sans-serif" font-size="12" lengthAdjust="spacing" textLength="33" x="275" y="534.0801">(VCF)</text><line style="stroke:#181818;stroke-width:1.5;" x1="130" x2="369" y1="722.7461" y2="722.7461"/><polygon fill="#F1F1F1" points="208.5,244.4688,287.5,244.4688,299.5,256.4688,287.5,268.4688,208.5,268.4688,196.5,256.4688,208.5,244.4688" style="stroke:#181818;stroke-width:0.5;"/><text fill="#000000" font-family="sans-serif" font-size="11" lengthAdjust="spacing" textLength="23" x="252" y="278.6792">true</text><text fill="#000000" font-family="sans-serif" font-size="11" lengthAdjust="spacing" textLength="79" x="208.5" y="260.2769">run_discovery</text><text fill="#000000" font-family="sans-serif" font-size="11" lengthAdjust="spacing" textLength="28" x="299.5" y="253.8745">false</text><polygon fill="#F1F1F1" points="248,742.7461,260,754.7461,248,766.7461,236,754.7461,248,742.7461" style="stroke:#181818;stroke-width:0.5;"/><ellipse cx="248" cy="797.7461" rx="11" ry="11" style="stroke:#222222;stroke-width:1.0;fill:none;"/><ellipse cx="248" cy="797.7461" fill="#222222" rx="6" ry="6" style="stroke:#111111;stroke-width:1.0;"/><line style="stroke:#181818;stroke-width:1.5;" x1="638" x2="1036.5" y1="440.2227" y2="440.2227"/><path d="M735,480.1094 L735,503.8086 L715,507.8086 L735,511.8086 L735,535.5078 A0,0 0 0 0 735,535.5078 L816,535.5078 A0,0 0 0 0 816,535.5078 L816,490.1094 L806,480.1094 L735,480.1094 A0,0 0 0 0 735,480.1094 " fill="#FEFFDD" style="stroke:#181818;stroke-width:0.5;"/><path d="M806,480.1094 L806,490.1094 L816,490.1094 L806,480.1094 " fill="#FEFFDD" style="stroke:#181818;stroke-width:0.5;"/><text fill="#000000" font-family="sans-serif" font-size="13" lengthAdjust="spacing" textLength="32" x="741" y="497.1763">input</text><text fill="#000000" font-family="sans-serif" font-size="13" lengthAdjust="spacing" textLength="50" x="741" y="512.3091">merged</text><text fill="#000000" font-family="sans-serif" font-size="13" lengthAdjust="spacing" textLength="60" x="741" y="527.4419">gSV sites</text><rect fill="#F1F1F1" height="92.1719" rx="12.5" ry="12.5" style="stroke:#181818;stroke-width:0.5;" width="154" x="561" y="461.7227"/><text fill="#000000" font-family="sans-serif" font-size="14" font-weight="bold" lengthAdjust="spacing" textLength="131" x="571" y="484.7178">Regenotype gSV</text><text fill="#000000" font-family="sans-serif" font-size="12" lengthAdjust="spacing" textLength="12" x="571" y="499.1582">---</text><text fill="#000000" font-family="sans-serif" font-size="12" lengthAdjust="spacing" textLength="102" x="571" y="513.127">Regenotype SVs</text><text fill="#000000" font-family="sans-serif" font-size="12" lengthAdjust="spacing" textLength="134" x="571" y="527.0957">using DELLY gSV calls</text><text fill="#000000" font-family="sans-serif" font-size="12" lengthAdjust="spacing" textLength="33" x="571" y="541.0645">(BCF)</text><path d="M844,480.1094 L844,535.5078 A0,0 0 0 0 844,535.5078 L935,535.5078 A0,0 0 0 0 935,535.5078 L935,511.8086 L955,507.8086 L935,503.8086 L935,490.1094 L925,480.1094 L844,480.1094 A0,0 0 0 0 844,480.1094 " fill="#FEFFDD" style="stroke:#181818;stroke-width:0.5;"/><path d="M925,480.1094 L925,490.1094 L935,490.1094 L925,480.1094 " fill="#FEFFDD" style="stroke:#181818;stroke-width:0.5;"/><text fill="#000000" font-family="sans-serif" font-size="13" lengthAdjust="spacing" textLength="32" x="850" y="497.1763">input</text><text fill="#000000" font-family="sans-serif" font-size="13" lengthAdjust="spacing" textLength="50" x="850" y="512.3091">merged</text><text fill="#000000" font-family="sans-serif" font-size="13" lengthAdjust="spacing" textLength="70" x="850" y="527.4419">gCNV sites</text><rect fill="#F1F1F1" height="92.1719" rx="12.5" ry="12.5" style="stroke:#181818;stroke-width:0.5;" width="163" x="955" y="461.7227"/><text fill="#000000" font-family="sans-serif" font-size="14" font-weight="bold" lengthAdjust="spacing" textLength="143" x="965" y="484.7178">Regenotype gCNV</text><text fill="#000000" font-family="sans-serif" font-size="12" lengthAdjust="spacing" textLength="12" x="965" y="499.1582">---</text><text fill="#000000" font-family="sans-serif" font-size="12" lengthAdjust="spacing" textLength="111" x="965" y="513.127">Regenotype CNVs</text><text fill="#000000" font-family="sans-serif" font-size="12" lengthAdjust="spacing" textLength="143" x="965" y="527.0957">using DELLY gCNV calls</text><text fill="#000000" font-family="sans-serif" font-size="12" lengthAdjust="spacing" textLength="33" x="965" y="541.0645">(BCF)</text><line style="stroke:#181818;stroke-width:1.5;" x1="638" x2="1036.5" y1="573.8945" y2="573.8945"/><polygon fill="#F1F1F1" points="790,391.8203,889,391.8203,901,403.8203,889,415.8203,790,415.8203,778,403.8203,790,391.8203" style="stroke:#181818;stroke-width:0.5;"/><text fill="#000000" font-family="sans-serif" font-size="11" lengthAdjust="spacing" textLength="23" x="843.5" y="426.0308">true</text><text 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@startuml
skinparam SwimlaneTitleFontStyle bold

start

:==Normal BAM
- - -
Input Normal BAM;
:==Input Validation
- - -
Validate the input BAM and corresponding index file;
fork
if (run_discovery) is (true) then
    split
        :==DELLY gSV
        - - -
        Call germline SVs using DELLY
        (BCF);
        :==DELLY gCNV
        - - -
        Call germline CNVs using DELLY
        (BCF);
        :==QC
        - - -
        Quality Check variant calls;
        :==Output Validation
        - - -
        Validate BCF output;
    split again
        :==Manta gSV
        - - -
        Call germline SVs using Manta
        (VCF);
    end split
else (false)
endif
stop

fork again
if (run_regenotyping) is (true) then
    split
    :==Regenotype gSV
    - - -
    Regenotype SVs
    using DELLY gSV calls
    (BCF);
    note right: input\nmerged\ngSV sites
    split again
    :==Regenotype gCNV
    - - -
    Regenotype CNVs
    using DELLY gCNV calls
    (BCF);
    note left: input\nmerged\ngCNV sites
    end split

else (false)
endif
stop

@enduml

PlantUML version 1.2022.6(Tue Jun 21 17:34:49 GMT 2022)
(GPL source distribution)
Java Runtime: OpenJDK Runtime Environment
JVM: OpenJDK 64-Bit Server VM
Default Encoding: UTF-8
Language: en
Country: US
--></g></svg>