docs/calculate-targeted-coverage-flow.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="892px" preserveAspectRatio="none" style="width:1355px;height:892px;background:#FFFFFF;" version="1.1" viewBox="0 0 1355 892" width="1355px" zoomAndPan="magnify"><defs/><g><!--MD5=[5793b8a6652117c897ab2de440c96a33]
cluster Target-Focused Workflow--><g id="cluster_Target-Focused Workflow"><rect height="495" rx="2.5" ry="2.5" style="stroke:#181818;stroke-width:1.0;fill:none;" width="512" x="7" y="7"/><text fill="#000000" font-family="sans-serif" font-size="14" font-weight="bold" lengthAdjust="spacing" textLength="205" x="160.5" y="21.9951">Target-Focused Workflow</text></g><!--MD5=[d541b56f1a19ef419b51f0e2d36e069b]
cluster Input1--><g id="cluster_Input1"><rect height="68" rx="2.5" ry="2.5" style="stroke:#00000000;stroke-width:1.0;fill:none;" width="233" x="77" y="50"/><text fill="#000000" font-family="sans-serif" font-size="0" font-weight="bold" lengthAdjust="spacing" textLength="0" x="193.5" y="52">Input</text></g><!--MD5=[fdf0c65af9cafec17be4ce373e959a1e]
cluster Off-Target Workflow--><g id="cluster_Off-Target Workflow"><rect height="879" rx="2.5" ry="2.5" style="stroke:#181818;stroke-width:1.0;fill:none;" width="602" x="543" y="7"/><text fill="#000000" font-family="sans-serif" font-size="14" font-weight="bold" lengthAdjust="spacing" textLength="162" x="763" y="21.9951">Off-Target Workflow</text></g><!--MD5=[fcfe6af240cbb9de2e31d0010bc81b0a]
cluster Input2--><g id="cluster_Input2"><rect height="68" rx="2.5" ry="2.5" style="stroke:#00000000;stroke-width:1.0;fill:none;" width="343" x="664" y="50"/><text fill="#000000" font-family="sans-serif" font-size="0" font-weight="bold" lengthAdjust="spacing" textLength="0" x="835.5" y="52">Input</text></g><!--MD5=[f7217341b3bb6bbf768c7f0e049f8d09]
cluster Legend--><g id="cluster_Legend"><rect height="375" rx="2.5" ry="2.5" style="stroke:#181818;stroke-width:1.0;fill:none;" width="180" x="1169" y="31"/><text fill="#000000" font-family="sans-serif" font-size="14" font-weight="bold" lengthAdjust="spacing" textLength="59" x="1229.5" y="45.9951">Legend</text></g><!--MD5=[a83f4c4b109093b6df97f2e5475fbb6d]
entity BAM1--><g id="elem_BAM1"><rect fill="#ADD8E6" height="36.2969" rx="2.5" ry="2.5" style="stroke:#181818;stroke-width:0.5;" width="51" x="355.5" y="66"/><text fill="#000000" font-family="sans-serif" font-size="14" lengthAdjust="spacing" textLength="31" x="365.5" y="88.9951">BAM</text></g><!--MD5=[afbb0db1cbcdc0e923b4432d737361e0]
entity ValInputs1--><g id="elem_ValInputs1"><rect fill="#D3D3D3" height="36.2969" rx="2.5" ry="2.5" style="stroke:#181818;stroke-width:0.5;" width="121" x="320.5" y="162"/><text fill="#000000" font-family="sans-serif" font-size="14" lengthAdjust="spacing" textLength="101" x="330.5" y="184.9951">Validate Inputs</text></g><!--MD5=[b3fc1d5769c32d62159879ccf9acacb3]
entity CalcReadDepth--><g id="elem_CalcReadDepth"><rect fill="#D3D3D3" height="36.2969" rx="2.5" ry="2.5" style="stroke:#181818;stroke-width:0.5;" width="237" x="265.5" y="258"/><text fill="#000000" font-family="sans-serif" font-size="14" lengthAdjust="spacing" textLength="217" x="275.5" y="280.9951">Calculate Per-Base Read Depth</text></g><!--MD5=[bd6c7db5d87a2d4a9d8c6ffd88a5bcea]
entity ConvBEDtoIntervalList--><g id="elem_ConvBEDtoIntervalList"><rect fill="#D3D3D3" height="36.2969" rx="2.5" ry="2.5" style="stroke:#181818;stroke-width:0.5;" width="202" x="29" y="162"/><text fill="#000000" font-family="sans-serif" font-size="14" lengthAdjust="spacing" textLength="182" x="39" y="184.9951">Convert BED to interval.list</text></g><!--MD5=[2c5b443c033a35a14a0a2ae3c89dfd10]
entity ConvtoBED1--><g id="elem_ConvtoBED1"><rect fill="#D3D3D3" height="36.2969" rx="2.5" ry="2.5" style="stroke:#181818;stroke-width:0.5;" width="126" x="321" y="354"/><text fill="#000000" font-family="sans-serif" font-size="14" lengthAdjust="spacing" textLength="106" x="331" y="376.9951">Convert to BED</text></g><!--MD5=[b356e89eaf00e777fdf024a4814b8e18]
entity CalcCovMetrics--><g id="elem_CalcCovMetrics"><rect fill="#D3D3D3" height="36.2969" rx="2.5" ry="2.5" style="stroke:#181818;stroke-width:0.5;" width="207" x="23.5" y="258"/><text fill="#000000" font-family="sans-serif" font-size="14" lengthAdjust="spacing" textLength="187" x="33.5" y="280.9951">Calculate Coverage Metrics</text></g><!--MD5=[dcd1f042f3b348163f3493299ca35159]
entity TargetReadDepthBED--><g id="elem_TargetReadDepthBED"><rect fill="#98FB98" height="36.2969" rx="2.5" ry="2.5" style="stroke:#181818;stroke-width:0.5;" width="212" x="278" y="450"/><text fill="#000000" font-family="sans-serif" font-size="14" lengthAdjust="spacing" textLength="192" x="288" y="472.9951">*target-depth-per-base.bed</text></g><!--MD5=[360be6d182cb7145dcbdee0021c8ccd3]
entity HSMetrics--><g id="elem_HSMetrics"><rect fill="#F5DEB3" height="36.2969" rx="2.5" ry="2.5" style="stroke:#181818;stroke-width:0.5;" width="117" x="68.5" y="354"/><text fill="#000000" font-family="sans-serif" font-size="14" lengthAdjust="spacing" textLength="97" x="78.5" y="376.9951">*HSMetrics.txt</text></g><!--MD5=[07ce715d8952035f1c648a97cce063ab]
entity TargetFile1--><g id="elem_TargetFile1"><rect fill="#ADD8E6" height="36.2969" rx="2.5" ry="2.5" style="stroke:#181818;stroke-width:0.5;" width="92" x="202" y="66"/><text fill="#000000" font-family="sans-serif" font-size="14" lengthAdjust="spacing" textLength="72" x="212" y="88.9951">Target File</text></g><!--MD5=[bb2b4fcf43ed25e0ab855486922ad703]
entity BaitFile--><g id="elem_BaitFile"><rect fill="#ADD8E6" height="36.2969" rx="2.5" ry="2.5" style="stroke:#181818;stroke-width:0.5;" width="73" x="93.5" y="66"/><text fill="#000000" font-family="sans-serif" font-size="14" lengthAdjust="spacing" textLength="53" x="103.5" y="88.9951">Bait File</text></g><!--MD5=[3711304ccc2c64bce48f9718f643142e]
entity ValInputs2--><g id="elem_ValInputs2"><rect fill="#D3D3D3" height="36.2969" rx="2.5" ry="2.5" style="stroke:#181818;stroke-width:0.5;" width="121" x="913.5" y="162"/><text fill="#000000" font-family="sans-serif" font-size="14" lengthAdjust="spacing" textLength="101" x="923.5" y="184.9951">Validate Inputs</text></g><!--MD5=[b6607c3669bb86c4076734be7bd06d49]
entity CalcReadDepthAtdbSNP--><g id="elem_CalcReadDepthAtdbSNP"><rect fill="#D3D3D3" height="36.2969" rx="2.5" ry="2.5" style="stroke:#181818;stroke-width:0.5;" width="272" x="843" y="258"/><text fill="#000000" font-family="sans-serif" font-size="14" lengthAdjust="spacing" textLength="252" x="853" y="280.9951">Cacluate Read Depth at dbSNP Sites</text></g><!--MD5=[5bda774f1e672053773e83dd05eacaed]
entity FilterReadDepth--><g id="elem_FilterReadDepth"><rect fill="#D3D3D3" height="36.2969" rx="2.5" ry="2.5" style="stroke:#181818;stroke-width:0.5;" width="228" x="884" y="450"/><text fill="#000000" font-family="sans-serif" font-size="14" lengthAdjust="spacing" textLength="208" x="894" y="472.9951">Filter for Minimum Read Depth</text></g><!--MD5=[cd6e518d9ba44279cfc888103d8aa6a4]
entity FilterOffTarget--><g id="elem_FilterOffTarget"><rect fill="#D3D3D3" height="36.2969" rx="2.5" ry="2.5" style="stroke:#181818;stroke-width:0.5;" width="186" x="646" y="450"/><text fill="#000000" font-family="sans-serif" font-size="14" lengthAdjust="spacing" textLength="166" x="656" y="472.9951">Filter for Off-Target Sites</text></g><!--MD5=[715b69296de685ae7f1f45cea8134010]
entity ConvtoBED2--><g id="elem_ConvtoBED2"><rect fill="#D3D3D3" height="36.2969" rx="2.5" ry="2.5" style="stroke:#181818;stroke-width:0.5;" width="126" x="916" y="354"/><text fill="#000000" font-family="sans-serif" font-size="14" lengthAdjust="spacing" textLength="106" x="926" y="376.9951">Convert to BED</text></g><!--MD5=[0c145ebd8b2b512a07df55d1a2465d38]
entity AddSlopOffTarget--><g id="elem_AddSlopOffTarget"><rect fill="#D3D3D3" height="36.2969" rx="2.5" ry="2.5" style="stroke:#181818;stroke-width:0.5;" width="212" x="917" y="546"/><text fill="#000000" font-family="sans-serif" font-size="14" lengthAdjust="spacing" textLength="192" x="927" y="568.9951">Add Slop to Off-Target SNPs</text></g><!--MD5=[f50d1513eea2cf224a813b3b0f46f551]
entity MergeWithTarget--><g id="elem_MergeWithTarget"><rect fill="#D3D3D3" height="36.2969" rx="2.5" ry="2.5" style="stroke:#181818;stroke-width:0.5;" width="172" x="758" y="642"/><text fill="#000000" font-family="sans-serif" font-size="14" lengthAdjust="spacing" textLength="152" x="768" y="664.9951">Merge with Target File</text></g><!--MD5=[6b0d55934776f8df877a4aa9a84c95b4]
entity AddSlopTarget--><g id="elem_AddSlopTarget"><rect fill="#D3D3D3" height="36.2969" rx="2.5" ry="2.5" style="stroke:#181818;stroke-width:0.5;" width="209" x="598.5" y="258"/><text fill="#000000" font-family="sans-serif" font-size="14" lengthAdjust="spacing" textLength="189" x="608.5" y="280.9951">Add Slop to Target Intervals</text></g><!--MD5=[97b99327512678a3edfd748478556652]
entity TargetPlusOffTargetReadDepthBED--><g id="elem_TargetPlusOffTargetReadDepthBED"><rect fill="#98FB98" height="36.2969" rx="2.5" ry="2.5" style="stroke:#181818;stroke-width:0.5;" width="328" x="680" y="738"/><text fill="#000000" font-family="sans-serif" font-size="14" lengthAdjust="spacing" textLength="308" x="690" y="760.9951">*target-with-enriched-off-target-intervals.bed</text></g><!--MD5=[7f5ec864b4cb369ae6c755b0ecd8ff52]
entity OffTargetReadDepth--><g id="elem_OffTargetReadDepth"><rect fill="#98FB98" height="36.2969" rx="2.5" ry="2.5" style="stroke:#181818;stroke-width:0.5;" width="285" x="596.5" y="546"/><text fill="#000000" font-family="sans-serif" font-size="14" lengthAdjust="spacing" textLength="265" x="606.5" y="568.9951">*off-target-dbSNP-depth-per-base.bed</text></g><!--MD5=[e94e62f06dcbdb4a6e54560988436e02]
entity RecalBAM--><g id="elem_RecalBAM"><rect fill="#FFFFFF" height="36.2969" rx="2.5" ry="2.5" style="stroke:#181818;stroke-width:0.5;" width="128" x="780" y="834"/><text fill="#000000" font-family="sans-serif" font-size="14" lengthAdjust="spacing" textLength="108" x="790" y="856.9951">recalibrate-BAM</text></g><!--MD5=[d240438f19e54a6f2cb3889e6527a070]
entity TargetFile2--><g id="elem_TargetFile2"><rect fill="#ADD8E6" height="36.2969" rx="2.5" ry="2.5" style="stroke:#181818;stroke-width:0.5;" width="92" x="680" y="66"/><text fill="#000000" font-family="sans-serif" font-size="14" lengthAdjust="spacing" textLength="72" x="690" y="88.9951">Target File</text></g><!--MD5=[7b92cfaf277f583add5cf6dde83011d4]
entity dbSNP_VCF--><g id="elem_dbSNP_VCF"><rect fill="#ADD8E6" height="36.2969" rx="2.5" ry="2.5" style="stroke:#181818;stroke-width:0.5;" width="97" x="807.5" y="66"/><text fill="#000000" font-family="sans-serif" font-size="14" lengthAdjust="spacing" textLength="77" x="817.5" y="88.9951">dbSNP VCF</text></g><!--MD5=[0b8015d1c6b7568455913bd022baae3a]
entity BAM2--><g id="elem_BAM2"><rect fill="#ADD8E6" height="36.2969" rx="2.5" ry="2.5" style="stroke:#181818;stroke-width:0.5;" width="51" x="939.5" y="66"/><text fill="#000000" font-family="sans-serif" font-size="14" lengthAdjust="spacing" textLength="31" x="949.5" y="88.9951">BAM</text></g><!--MD5=[486a548dd2b54905abbe5c1ab7fa9983]
entity IF--><g id="elem_IF"><rect fill="#ADD8E6" height="36.2969" rx="2.5" ry="2.5" style="stroke:#181818;stroke-width:0.5;" width="82" x="1218" y="66"/><text fill="#000000" font-family="sans-serif" font-size="14" lengthAdjust="spacing" textLength="62" x="1228" y="88.9951">Input File</text></g><!--MD5=[d3ef473a5067122b9254af2bc2f25065]
entity QC--><g id="elem_QC"><rect fill="#F5DEB3" height="36.2969" rx="2.5" ry="2.5" style="stroke:#181818;stroke-width:0.5;" width="147" x="1185.5" y="162"/><text fill="#000000" font-family="sans-serif" font-size="14" lengthAdjust="spacing" textLength="127" x="1195.5" y="184.9951">Quality Control File</text></g><!--MD5=[633fdf3c843eeff0d0fbc3bde364bced]
entity OF--><g id="elem_OF"><rect fill="#98FB98" height="36.2969" rx="2.5" ry="2.5" style="stroke:#181818;stroke-width:0.5;" width="95" x="1211.5" y="258"/><text fill="#000000" font-family="sans-serif" font-size="14" lengthAdjust="spacing" textLength="75" x="1221.5" y="280.9951">Output File</text></g><!--MD5=[7842cb4300efb401920d8f72ebe921e6]
entity PS--><g id="elem_PS"><rect fill="#D3D3D3" height="36.2969" rx="2.5" ry="2.5" style="stroke:#181818;stroke-width:0.5;" width="112" x="1203" y="354"/><text fill="#000000" font-family="sans-serif" font-size="14" lengthAdjust="spacing" textLength="92" x="1213" y="376.9951">Process Step</text></g><!--MD5=[4ebbafa84b39c454a0f1728fb61efbcb]
link BAM1 to ValInputs1--><g id="link_BAM1_ValInputs1"><path d="M381,102.24 C381,117.48 381,139.81 381,156.46 " fill="none" id="BAM1-to-ValInputs1" style="stroke:#181818;stroke-width:1.0;"/><polygon fill="#181818" points="381,161.87,385,152.87,381,156.87,377,152.87,381,161.87" style="stroke:#181818;stroke-width:1.0;"/></g><!--MD5=[0b188298c9b1afe471d4865e17af690e]
link BaitFile to ConvBEDtoIntervalList--><g id="link_BaitFile_ConvBEDtoIntervalList"><path d="M130,102.24 C130,117.48 130,139.81 130,156.46 " fill="none" id="BaitFile-to-ConvBEDtoIntervalList" style="stroke:#181818;stroke-width:1.0;"/><polygon fill="#181818" points="130,161.87,134,152.87,130,156.87,126,152.87,130,161.87" style="stroke:#181818;stroke-width:1.0;"/></g><!--MD5=[a98f2fcb5fff3f38e9b30ea7ce7944cc]
reverse link BaitFile to TargetFile1--><g id="link_BaitFile_TargetFile1"><path d="M172.05,84 C181.94,84 191.84,84 201.73,84 " fill="none" id="BaitFile-backto-TargetFile1" style="stroke:#181818;stroke-width:1.0;"/><polygon fill="#181818" points="166.88,84,175.8914,87.9743,171.88,83.9857,175.8685,79.9743,166.88,84" style="stroke:#181818;stroke-width:1.0;"/></g><!--MD5=[8613a7106181726335c268ad9afcbade]
link TargetFile1 to ConvBEDtoIntervalList--><g id="link_TargetFile1_ConvBEDtoIntervalList"><path d="M226.63,102.02 C206.71,117.89 176.96,141.59 155.73,158.5 " fill="none" id="TargetFile1-to-ConvBEDtoIntervalList" style="stroke:#181818;stroke-width:1.0;"/><polygon fill="#181818" points="151.61,161.79,161.1433,159.3167,155.5227,158.677,156.1624,153.0564,151.61,161.79" style="stroke:#181818;stroke-width:1.0;"/></g><!--MD5=[1ebea33f9c8662e739debdf82176c56c]
link TargetFile1 to CalcReadDepth--><g id="link_TargetFile1_CalcReadDepth"><path d="M254.11,102.13 C262.83,125.22 280.32,167.01 303,198 C318.64,219.36 340.61,239.83 357.73,254.28 " fill="none" id="TargetFile1-to-CalcReadDepth" style="stroke:#181818;stroke-width:1.0;"/><polygon fill="#181818" points="361.97,257.82,357.6329,248.9775,358.1347,254.6121,352.5002,255.1139,361.97,257.82" style="stroke:#181818;stroke-width:1.0;"/></g><!--MD5=[f308aad7a2b7b7a038ef70c2e5184697]
link ConvBEDtoIntervalList to CalcCovMetrics--><g id="link_ConvBEDtoIntervalList_CalcCovMetrics"><path d="M129.45,198.24 C128.96,213.48 128.25,235.81 127.72,252.46 " fill="none" id="ConvBEDtoIntervalList-to-CalcCovMetrics" style="stroke:#181818;stroke-width:1.0;"/><polygon fill="#181818" points="127.55,257.87,131.856,249.0123,127.7213,252.8729,123.8607,248.7382,127.55,257.87" style="stroke:#181818;stroke-width:1.0;"/></g><!--MD5=[ea8d0339758d2104072632f00f4bc0a1]
link ValInputs1 to CalcReadDepth--><g id="link_ValInputs1_CalcReadDepth"><path d="M381.55,198.24 C382.04,213.48 382.75,235.81 383.28,252.46 " fill="none" id="ValInputs1-to-CalcReadDepth" style="stroke:#181818;stroke-width:1.0;"/><polygon fill="#181818" points="383.45,257.87,387.1393,248.7382,383.2787,252.8729,379.144,249.0123,383.45,257.87" style="stroke:#181818;stroke-width:1.0;"/></g><!--MD5=[8836070171cd6f0734a3a2db1cce46c0]
link ValInputs1 to CalcCovMetrics--><g id="link_ValInputs1_CalcCovMetrics"><path d="M335,198.02 C290.73,214.41 223.9,239.14 178.01,256.12 " fill="none" id="ValInputs1-to-CalcCovMetrics" style="stroke:#181818;stroke-width:1.0;"/><polygon fill="#181818" points="173.08,257.95,182.9082,258.5879,177.771,256.2195,180.1394,251.0823,173.08,257.95" style="stroke:#181818;stroke-width:1.0;"/></g><!--MD5=[d676bc7e0090eb72ce6e5be50a2e077f]
link CalcCovMetrics to HSMetrics--><g id="link_CalcCovMetrics_HSMetrics"><path d="M127,294.24 C127,309.48 127,331.81 127,348.46 " fill="none" id="CalcCovMetrics-to-HSMetrics" style="stroke:#181818;stroke-width:1.0;"/><polygon fill="#181818" points="127,353.87,131,344.87,127,348.87,123,344.87,127,353.87" style="stroke:#181818;stroke-width:1.0;"/></g><!--MD5=[01f923ac9ec9e6500d1bb9fa79e1697e]
link CalcReadDepth to ConvtoBED1--><g id="link_CalcReadDepth_ConvtoBED1"><path d="M384,294.24 C384,309.48 384,331.81 384,348.46 " fill="none" id="CalcReadDepth-to-ConvtoBED1" style="stroke:#181818;stroke-width:1.0;"/><polygon fill="#181818" points="384,353.87,388,344.87,384,348.87,380,344.87,384,353.87" style="stroke:#181818;stroke-width:1.0;"/></g><!--MD5=[af6509568e048ae4cd4a149100a354eb]
link ConvtoBED1 to TargetReadDepthBED--><g id="link_ConvtoBED1_TargetReadDepthBED"><path d="M384,390.24 C384,405.48 384,427.81 384,444.46 " fill="none" id="ConvtoBED1-to-TargetReadDepthBED" style="stroke:#181818;stroke-width:1.0;"/><polygon fill="#181818" points="384,449.87,388,440.87,384,444.87,380,440.87,384,449.87" style="stroke:#181818;stroke-width:1.0;"/></g><!--MD5=[ad70a8f2d24c7fbe93a363248ba8fd89]
link TargetFile2 to AddSlopTarget--><g id="link_TargetFile2_AddSlopTarget"><path d="M723.92,102.2 C719.74,136.67 710.36,214.23 705.71,252.61 " fill="none" id="TargetFile2-to-AddSlopTarget" style="stroke:#181818;stroke-width:1.0;"/><polygon fill="#181818" points="705.06,257.98,710.1096,249.5241,705.6591,253.016,702.1672,248.5656,705.06,257.98" style="stroke:#181818;stroke-width:1.0;"/></g><!--MD5=[bb9b1f52b6b7f984ba4d3d204d33fcda]
link TargetFile2 to MergeWithTarget--><g id="link_TargetFile2_MergeWithTarget"><path d="M694.78,102.04 C646.69,130.83 560,193.97 560,275 C560,275 560,275 560,469 C560,519.93 545.14,543.96 579,582 C622.37,630.72 694.55,649.4 752.64,656.21 " fill="none" id="TargetFile2-to-MergeWithTarget" style="stroke:#181818;stroke-width:1.0;"/><polygon fill="#181818" points="757.86,656.79,749.3615,651.8125,752.8911,656.2331,748.4705,659.7628,757.86,656.79" style="stroke:#181818;stroke-width:1.0;"/></g><!--MD5=[0f5f9f541059e0d392cad8edec1088b0]
link dbSNP_VCF to CalcReadDepthAtdbSNP--><g id="link_dbSNP_VCF_CalcReadDepthAtdbSNP"><path d="M859.38,102.24 C864.52,125.46 875.88,167.39 896,198 C910.66,220.29 933.1,240.59 950.96,254.75 " fill="none" id="dbSNP_VCF-to-CalcReadDepthAtdbSNP" style="stroke:#181818;stroke-width:1.0;"/><polygon fill="#181818" points="954.93,257.85,950.3077,249.1532,950.9925,254.7685,945.3772,255.4532,954.93,257.85" style="stroke:#181818;stroke-width:1.0;"/></g><!--MD5=[1085dcdb1e044111634ab5f4c085fbb6]
link BAM2 to ValInputs2--><g id="link_BAM2_ValInputs2"><path d="M966.65,102.24 C968.12,117.61 970.28,140.2 971.88,156.89 " fill="none" id="BAM2-to-ValInputs2" style="stroke:#181818;stroke-width:1.0;"/><polygon fill="#181818" points="972.36,161.87,975.4685,152.5246,971.8752,156.8936,967.5062,153.3003,972.36,161.87" style="stroke:#181818;stroke-width:1.0;"/></g><!--MD5=[26102ab38cefa976c6f11175f31d78b3]
link ValInputs2 to CalcReadDepthAtdbSNP--><g id="link_ValInputs2_CalcReadDepthAtdbSNP"><path d="M974.92,198.24 C975.73,213.48 976.92,235.81 977.8,252.46 " fill="none" id="ValInputs2-to-CalcReadDepthAtdbSNP" style="stroke:#181818;stroke-width:1.0;"/><polygon fill="#181818" points="978.09,257.87,981.5948,248.6659,977.8182,252.8774,973.6067,249.1008,978.09,257.87" style="stroke:#181818;stroke-width:1.0;"/></g><!--MD5=[bc906825f7e1d5b70f40674632bccb60]
link AddSlopTarget to FilterOffTarget--><g id="link_AddSlopTarget_FilterOffTarget"><path d="M706.26,294.2 C712.79,328.67 727.49,406.23 734.76,444.61 " fill="none" id="AddSlopTarget-to-FilterOffTarget" style="stroke:#181818;stroke-width:1.0;"/><polygon fill="#181818" points="735.78,449.98,738.0394,440.3938,734.8517,445.0669,730.1785,441.8792,735.78,449.98" style="stroke:#181818;stroke-width:1.0;"/></g><!--MD5=[e6ec3830f61b2fc00c1f964c6c082250]
link CalcReadDepthAtdbSNP to ConvtoBED2--><g id="link_CalcReadDepthAtdbSNP_ConvtoBED2"><path d="M979,294.24 C979,309.48 979,331.81 979,348.46 " fill="none" id="CalcReadDepthAtdbSNP-to-ConvtoBED2" style="stroke:#181818;stroke-width:1.0;"/><polygon fill="#181818" points="979,353.87,983,344.87,979,348.87,975,344.87,979,353.87" style="stroke:#181818;stroke-width:1.0;"/></g><!--MD5=[312c39a7f5e428ae64e27424907166bd]
link ConvtoBED2 to FilterOffTarget--><g id="link_ConvtoBED2_FilterOffTarget"><path d="M935.54,390.02 C893.7,406.41 830.56,431.14 787.2,448.12 " fill="none" id="ConvtoBED2-to-FilterOffTarget" style="stroke:#181818;stroke-width:1.0;"/><polygon fill="#181818" points="782.54,449.95,792.3793,450.384,787.1941,448.1226,789.4555,442.9374,782.54,449.95" style="stroke:#181818;stroke-width:1.0;"/></g><!--MD5=[ea959455ce9951d3e4721f89ee60932b]
link ConvtoBED2 to FilterReadDepth--><g id="link_ConvtoBED2_FilterReadDepth"><path d="M982.48,390.24 C985.59,405.61 990.16,428.2 993.53,444.89 " fill="none" id="ConvtoBED2-to-FilterReadDepth" style="stroke:#181818;stroke-width:1.0;"/><polygon fill="#181818" points="994.54,449.87,996.6865,440.2579,993.5539,444.9682,988.8436,441.8356,994.54,449.87" style="stroke:#181818;stroke-width:1.0;"/></g><!--MD5=[0e0a99d1d7bc0797a534b161d1c3fca8]
link FilterReadDepth to AddSlopOffTarget--><g id="link_FilterReadDepth_AddSlopOffTarget"><path d="M1002.59,486.24 C1006.67,501.61 1012.68,524.2 1017.12,540.89 " fill="none" id="FilterReadDepth-to-AddSlopOffTarget" style="stroke:#181818;stroke-width:1.0;"/><polygon fill="#181818" points="1018.44,545.87,1019.9896,536.1438,1017.1535,541.0384,1012.2589,538.2023,1018.44,545.87" style="stroke:#181818;stroke-width:1.0;"/></g><!--MD5=[1fe930d4fe042d6de6dd8d043965d9f2]
link FilterOffTarget to OffTargetReadDepth--><g id="link_FilterOffTarget_OffTargetReadDepth"><path d="M739,486.24 C739,501.48 739,523.81 739,540.46 " fill="none" id="FilterOffTarget-to-OffTargetReadDepth" style="stroke:#181818;stroke-width:1.0;"/><polygon fill="#181818" points="739,545.87,743,536.87,739,540.87,735,536.87,739,545.87" style="stroke:#181818;stroke-width:1.0;"/></g><!--MD5=[be633c3fef0ea7de7d91abfc3ce66e7d]
link AddSlopOffTarget to MergeWithTarget--><g id="link_AddSlopOffTarget_MergeWithTarget"><path d="M990.58,582.02 C959.76,598.21 913.43,622.54 881.14,639.5 " fill="none" id="AddSlopOffTarget-to-MergeWithTarget" style="stroke:#181818;stroke-width:1.0;"/><polygon fill="#181818" points="876.48,641.95,886.3075,641.3019,880.9055,639.623,882.5844,634.221,876.48,641.95" style="stroke:#181818;stroke-width:1.0;"/></g><!--MD5=[0fa50402f24eb397243c00d2dc3ff62f]
link MergeWithTarget to TargetPlusOffTargetReadDepthBED--><g id="link_MergeWithTarget_TargetPlusOffTargetReadDepthBED"><path d="M844,678.24 C844,693.48 844,715.81 844,732.46 " fill="none" id="MergeWithTarget-to-TargetPlusOffTargetReadDepthBED" style="stroke:#181818;stroke-width:1.0;"/><polygon fill="#181818" points="844,737.87,848,728.87,844,732.87,840,728.87,844,737.87" style="stroke:#181818;stroke-width:1.0;"/></g><!--MD5=[4737fbc0abd4b31898a08a11d07ff5b8]
link TargetPlusOffTargetReadDepthBED to RecalBAM--><g id="link_TargetPlusOffTargetReadDepthBED_RecalBAM"><path d="M844,774.24 C844,789.48 844,811.81 844,828.46 " fill="none" id="TargetPlusOffTargetReadDepthBED-to-RecalBAM" style="stroke:#181818;stroke-width:1.0;"/><polygon fill="#181818" points="844,833.87,848,824.87,844,828.87,840,824.87,844,833.87" style="stroke:#181818;stroke-width:1.0;"/></g><!--MD5=[1d4d0dbdd50de0a0980321eccab73fac]
link IF to QC--><!--MD5=[03c241bed99ac1776e7d8c4bd4f5cca5]
link QC to OF--><!--MD5=[35700df3515afd241139af4c0386ffe2]
link OF to PS--><!--MD5=[b8e815e99e79e7c975214b5ce20b9ed4]
@startuml
hide stereotype

skinparam rectangle {
    BackgroundColor<<InputFile>> #LightBlue
    BackgroundColor<<QCFile>> #Wheat
    BackgroundColor<<OutputFile>> #PaleGreen
    BackgroundColor<<ProcessStep>> #LightGray
    BorderColor<<transparent>> transparent
    FontSize<<transparent>> 0
}

' target workflow
rectangle "Target-Focused Workflow" {
    ' input
    rectangle Input as Input1 <<transparent>> {
        rectangle "Target File" as TargetFile1 <<InputFile>>
        rectangle "Bait File" as BaitFile <<InputFile>>
    }
    ' process steps
    rectangle "BAM" as BAM1 <<InputFile>>
    rectangle "Validate Inputs" as ValInputs1 <<ProcessStep>>
    rectangle "Calculate Per-Base Read Depth" as CalcReadDepth <<ProcessStep>>
    rectangle "Convert BED to interval.list" as ConvBEDtoIntervalList <<ProcessStep>>
    rectangle "Convert to BED" as ConvtoBED1 <<ProcessStep>>
    rectangle "Calculate Coverage Metrics" as CalcCovMetrics <<ProcessStep>>
    ' output files
    rectangle "~*target-depth-per-base.bed" as TargetReadDepthBED <<OutputFile>>
    ' QC files
    rectangle "~*HSMetrics.txt" as HSMetrics <<QCFile>>
}


' off target workflow
rectangle "Off-Target Workflow" {
    ' input
    rectangle Input as Input2 <<transparent>> {
        rectangle "Target File" as TargetFile2 <<InputFile>>
        rectangle "dbSNP VCF" as dbSNP_VCF <<InputFile>>
        rectangle "BAM" as BAM2 <<InputFile>>
    }
    ' process steps
    rectangle "Validate Inputs" as ValInputs2 <<ProcessStep>>
    rectangle "Cacluate Read Depth at dbSNP Sites" as CalcReadDepthAtdbSNP <<ProcessStep>>
    rectangle "Filter for Minimum Read Depth" as FilterReadDepth <<ProcessStep>>
    rectangle "Filter for Off-Target Sites" as FilterOffTarget <<ProcessStep>>
    rectangle "Convert to BED" as ConvtoBED2 <<ProcessStep>>
    rectangle "Add Slop to Off-Target SNPs" as AddSlopOffTarget <<ProcessStep>>
    rectangle "Merge with Target File" as MergeWithTarget <<ProcessStep>>
    rectangle "Add Slop to Target Intervals" as AddSlopTarget <<ProcessStep>>

    ' output files
    rectangle "~*target-with-enriched-off-target-intervals.bed" as TargetPlusOffTargetReadDepthBED <<OutputFile>>
    rectangle "~*off-target-dbSNP-depth-per-base.bed" as OffTargetReadDepth <<OutputFile>>

    ' end node
    rectangle "recalibrate-BAM" as RecalBAM #White
}


' Target Focused Workflow
' input
BAM1 - -> ValInputs1
BaitFile - -> ConvBEDtoIntervalList
TargetFile1 -l-> BaitFile
TargetFile1 - -> ConvBEDtoIntervalList
TargetFile1 - -> CalcReadDepth

ConvBEDtoIntervalList - -> CalcCovMetrics

ValInputs1 - -> CalcReadDepth
ValInputs1 - -> CalcCovMetrics

CalcCovMetrics - -> HSMetrics

CalcReadDepth - -> ConvtoBED1
ConvtoBED1 - -> TargetReadDepthBED


' Off-Target Workflow
' input
TargetFile2 - - -> AddSlopTarget
TargetFile2 - - -> MergeWithTarget
dbSNP_VCF - -> CalcReadDepthAtdbSNP
BAM2 - -> ValInputs2

ValInputs2 - -> CalcReadDepthAtdbSNP
AddSlopTarget - -> FilterOffTarget

CalcReadDepthAtdbSNP - -> ConvtoBED2

ConvtoBED2 - -> FilterOffTarget
ConvtoBED2 - -> FilterReadDepth

FilterReadDepth - -> AddSlopOffTarget
FilterOffTarget - -> OffTargetReadDepth

AddSlopOffTarget - -> MergeWithTarget

MergeWithTarget - -> TargetPlusOffTargetReadDepthBED

TargetPlusOffTargetReadDepthBED - -> RecalBAM


' Legend
rectangle Legend {
    rectangle "Input File" as IF <<InputFile>>
    rectangle "Quality Control File" as QC <<QCFile>>
    rectangle "Output File" as OF <<OutputFile>>
    rectangle "Process Step" as PS <<ProcessStep>>
}

IF -[hidden]-> QC
QC -[hidden]-> OF
OF -[hidden]-> PS

@enduml

@startuml
hide stereotype

skinparam rectangle {
    BackgroundColor<<InputFile>> #LightBlue
    BackgroundColor<<QCFile>> #Wheat
    BackgroundColor<<OutputFile>> #PaleGreen
    BackgroundColor<<ProcessStep>> #LightGray
    BorderColor<<transparent>> transparent
    FontSize<<transparent>> 0
}

rectangle "Target-Focused Workflow" {
    rectangle Input as Input1 <<transparent>> {
        rectangle "Target File" as TargetFile1 <<InputFile>>
        rectangle "Bait File" as BaitFile <<InputFile>>
    }
    rectangle "BAM" as BAM1 <<InputFile>>
    rectangle "Validate Inputs" as ValInputs1 <<ProcessStep>>
    rectangle "Calculate Per-Base Read Depth" as CalcReadDepth <<ProcessStep>>
    rectangle "Convert BED to interval.list" as ConvBEDtoIntervalList <<ProcessStep>>
    rectangle "Convert to BED" as ConvtoBED1 <<ProcessStep>>
    rectangle "Calculate Coverage Metrics" as CalcCovMetrics <<ProcessStep>>
    rectangle "~*target-depth-per-base.bed" as TargetReadDepthBED <<OutputFile>>
    rectangle "~*HSMetrics.txt" as HSMetrics <<QCFile>>
}


rectangle "Off-Target Workflow" {
    rectangle Input as Input2 <<transparent>> {
        rectangle "Target File" as TargetFile2 <<InputFile>>
        rectangle "dbSNP VCF" as dbSNP_VCF <<InputFile>>
        rectangle "BAM" as BAM2 <<InputFile>>
    }
    rectangle "Validate Inputs" as ValInputs2 <<ProcessStep>>
    rectangle "Cacluate Read Depth at dbSNP Sites" as CalcReadDepthAtdbSNP <<ProcessStep>>
    rectangle "Filter for Minimum Read Depth" as FilterReadDepth <<ProcessStep>>
    rectangle "Filter for Off-Target Sites" as FilterOffTarget <<ProcessStep>>
    rectangle "Convert to BED" as ConvtoBED2 <<ProcessStep>>
    rectangle "Add Slop to Off-Target SNPs" as AddSlopOffTarget <<ProcessStep>>
    rectangle "Merge with Target File" as MergeWithTarget <<ProcessStep>>
    rectangle "Add Slop to Target Intervals" as AddSlopTarget <<ProcessStep>>

    rectangle "~*target-with-enriched-off-target-intervals.bed" as TargetPlusOffTargetReadDepthBED <<OutputFile>>
    rectangle "~*off-target-dbSNP-depth-per-base.bed" as OffTargetReadDepth <<OutputFile>>

    rectangle "recalibrate-BAM" as RecalBAM #White
}


BAM1 - -> ValInputs1
BaitFile - -> ConvBEDtoIntervalList
TargetFile1 -l-> BaitFile
TargetFile1 - -> ConvBEDtoIntervalList
TargetFile1 - -> CalcReadDepth

ConvBEDtoIntervalList - -> CalcCovMetrics

ValInputs1 - -> CalcReadDepth
ValInputs1 - -> CalcCovMetrics

CalcCovMetrics - -> HSMetrics

CalcReadDepth - -> ConvtoBED1
ConvtoBED1 - -> TargetReadDepthBED


TargetFile2 - - -> AddSlopTarget
TargetFile2 - - -> MergeWithTarget
dbSNP_VCF - -> CalcReadDepthAtdbSNP
BAM2 - -> ValInputs2

ValInputs2 - -> CalcReadDepthAtdbSNP
AddSlopTarget - -> FilterOffTarget

CalcReadDepthAtdbSNP - -> ConvtoBED2

ConvtoBED2 - -> FilterOffTarget
ConvtoBED2 - -> FilterReadDepth

FilterReadDepth - -> AddSlopOffTarget
FilterOffTarget - -> OffTargetReadDepth

AddSlopOffTarget - -> MergeWithTarget

MergeWithTarget - -> TargetPlusOffTargetReadDepthBED

TargetPlusOffTargetReadDepthBED - -> RecalBAM


rectangle Legend {
    rectangle "Input File" as IF <<InputFile>>
    rectangle "Quality Control File" as QC <<QCFile>>
    rectangle "Output File" as OF <<OutputFile>>
    rectangle "Process Step" as PS <<ProcessStep>>
}

IF -[hidden]-> QC
QC -[hidden]-> OF
OF -[hidden]-> PS

@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>