imgs/dag.svg

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<!-- Title: snakemake_dag Pages: 1 -->
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<!-- 1 -->
<g id="node2" class="node">
<title>1</title>
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<!-- 1&#45;&gt;0 -->
<g id="edge1" class="edge">
<title>1&#45;&gt;0</title>
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<!-- 2 -->
<g id="node3" class="node">
<title>2</title>
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<text text-anchor="middle" x="156" y="-159.5" font-family="sans" font-size="10.00">SelectVariants</text>
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<!-- 2&#45;&gt;1 -->
<g id="edge2" class="edge">
<title>2&#45;&gt;1</title>
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<!-- 3 -->
<g id="node4" class="node">
<title>3</title>
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<text text-anchor="middle" x="156" y="-231.5" font-family="sans" font-size="10.00">ApplyVQSR_snp</text>
</g>
<!-- 3&#45;&gt;2 -->
<g id="edge3" class="edge">
<title>3&#45;&gt;2</title>
<path fill="none" stroke="grey" stroke-width="2" d="M156,-215.7C156,-207.98 156,-198.71 156,-190.11"/>
<polygon fill="grey" stroke="grey" stroke-width="2" points="159.5,-190.1 156,-180.1 152.5,-190.1 159.5,-190.1"/>
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<!-- 4 -->
<g id="node5" class="node">
<title>4</title>
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<text text-anchor="middle" x="105" y="-303.5" font-family="sans" font-size="10.00">ApplyVQSR_indel</text>
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<!-- 4&#45;&gt;3 -->
<g id="edge4" class="edge">
<title>4&#45;&gt;3</title>
<path fill="none" stroke="grey" stroke-width="2" d="M117.61,-287.7C123.6,-279.47 130.88,-269.48 137.48,-260.42"/>
<polygon fill="grey" stroke="grey" stroke-width="2" points="140.48,-262.25 143.54,-252.1 134.82,-258.13 140.48,-262.25"/>
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<!-- 5 -->
<g id="node6" class="node">
<title>5</title>
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<text text-anchor="middle" x="142" y="-447.5" font-family="sans" font-size="10.00">MergeCohortVCFs</text>
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<!-- 5&#45;&gt;4 -->
<g id="edge6" class="edge">
<title>5&#45;&gt;4</title>
<path fill="none" stroke="grey" stroke-width="2" d="M121.18,-431.62C111.54,-422.2 101.11,-409.7 96,-396 88.6,-376.18 91.62,-352.24 96.08,-334.19"/>
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<!-- 24 -->
<g id="node25" class="node">
<title>24</title>
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<text text-anchor="middle" x="142" y="-375.5" font-family="sans" font-size="10.00">VQSR_indel</text>
</g>
<!-- 5&#45;&gt;24 -->
<g id="edge28" class="edge">
<title>5&#45;&gt;24</title>
<path fill="none" stroke="grey" stroke-width="2" d="M142,-431.7C142,-423.98 142,-414.71 142,-406.11"/>
<polygon fill="grey" stroke="grey" stroke-width="2" points="145.5,-406.1 142,-396.1 138.5,-406.1 145.5,-406.1"/>
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<!-- 25 -->
<g id="node26" class="node">
<title>25</title>
<path fill="none" stroke="#d8cb56" stroke-width="2" d="M228,-324C228,-324 186,-324 186,-324 180,-324 174,-318 174,-312 174,-312 174,-300 174,-300 174,-294 180,-288 186,-288 186,-288 228,-288 228,-288 234,-288 240,-294 240,-300 240,-300 240,-312 240,-312 240,-318 234,-324 228,-324"/>
<text text-anchor="middle" x="207" y="-303.5" font-family="sans" font-size="10.00">VQSR_snp</text>
</g>
<!-- 5&#45;&gt;25 -->
<g id="edge29" class="edge">
<title>5&#45;&gt;25</title>
<path fill="none" stroke="grey" stroke-width="2" d="M161.16,-431.57C170.61,-421.96 181.37,-409.3 188,-396 197.67,-376.62 202.43,-352.47 204.77,-334.22"/>
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<!-- 6 -->
<g id="node7" class="node">
<title>6</title>
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<text text-anchor="middle" x="142" y="-519.5" font-family="sans" font-size="10.00">GenotypeGVCFs</text>
</g>
<!-- 6&#45;&gt;5 -->
<g id="edge8" class="edge">
<title>6&#45;&gt;5</title>
<path fill="none" stroke="grey" stroke-width="2" d="M142,-503.7C142,-495.98 142,-486.71 142,-478.11"/>
<polygon fill="grey" stroke="grey" stroke-width="2" points="145.5,-478.1 142,-468.1 138.5,-478.1 145.5,-478.1"/>
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<!-- 7 -->
<g id="node8" class="node">
<title>7</title>
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<text text-anchor="middle" x="142" y="-591.5" font-family="sans" font-size="10.00">CombineGVCFs</text>
</g>
<!-- 7&#45;&gt;6 -->
<g id="edge9" class="edge">
<title>7&#45;&gt;6</title>
<path fill="none" stroke="grey" stroke-width="2" d="M142,-575.7C142,-567.98 142,-558.71 142,-550.11"/>
<polygon fill="grey" stroke="grey" stroke-width="2" points="145.5,-550.1 142,-540.1 138.5,-550.1 145.5,-550.1"/>
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<!-- 8 -->
<g id="node9" class="node">
<title>8</title>
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<text text-anchor="middle" x="70" y="-663.5" font-family="sans" font-size="10.00">MergeHaplotypeCaller</text>
</g>
<!-- 8&#45;&gt;7 -->
<g id="edge10" class="edge">
<title>8&#45;&gt;7</title>
<path fill="none" stroke="grey" stroke-width="2" d="M87.8,-647.7C96.6,-639.14 107.38,-628.66 117,-619.3"/>
<polygon fill="grey" stroke="grey" stroke-width="2" points="119.68,-621.58 124.41,-612.1 114.8,-616.57 119.68,-621.58"/>
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<!-- 9 -->
<g id="node10" class="node">
<title>9</title>
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<text text-anchor="middle" x="70" y="-735.5" font-family="sans" font-size="10.00">HaplotypeCaller</text>
</g>
<!-- 9&#45;&gt;8 -->
<g id="edge12" class="edge">
<title>9&#45;&gt;8</title>
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<polygon fill="grey" stroke="grey" stroke-width="2" points="73.5,-694.1 70,-684.1 66.5,-694.1 73.5,-694.1"/>
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<!-- 10 -->
<g id="node11" class="node">
<title>10</title>
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<text text-anchor="middle" x="61" y="-879.5" font-family="sans" font-size="10.00">SortBam</text>
</g>
<!-- 10&#45;&gt;9 -->
<g id="edge13" class="edge">
<title>10&#45;&gt;9</title>
<path fill="none" stroke="grey" stroke-width="2" d="M60.15,-863.9C59.46,-845.96 58.9,-816.94 61,-792 61.72,-783.5 63.07,-774.31 64.51,-766.01"/>
<polygon fill="grey" stroke="grey" stroke-width="2" points="67.97,-766.56 66.35,-756.09 61.09,-765.29 67.97,-766.56"/>
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<!-- 15 -->
<g id="node16" class="node">
<title>15</title>
<path fill="none" stroke="#56d873" stroke-width="2" d="M124,-828C124,-828 82,-828 82,-828 76,-828 70,-822 70,-816 70,-816 70,-804 70,-804 70,-798 76,-792 82,-792 82,-792 124,-792 124,-792 130,-792 136,-798 136,-804 136,-804 136,-816 136,-816 136,-822 130,-828 124,-828"/>
<text text-anchor="middle" x="103" y="-807.5" font-family="sans" font-size="10.00">IndexBam</text>
</g>
<!-- 10&#45;&gt;15 -->
<g id="edge19" class="edge">
<title>10&#45;&gt;15</title>
<path fill="none" stroke="grey" stroke-width="2" d="M71.38,-863.7C76.26,-855.56 82.19,-845.69 87.58,-836.7"/>
<polygon fill="grey" stroke="grey" stroke-width="2" points="90.59,-838.48 92.74,-828.1 84.59,-834.88 90.59,-838.48"/>
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<!-- 11 -->
<g id="node12" class="node">
<title>11</title>
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<text text-anchor="middle" x="61" y="-951.5" font-family="sans" font-size="10.00">GatherRecalBamFiles</text>
</g>
<!-- 11&#45;&gt;10 -->
<g id="edge15" class="edge">
<title>11&#45;&gt;10</title>
<path fill="none" stroke="grey" stroke-width="2" d="M61,-935.7C61,-927.98 61,-918.71 61,-910.11"/>
<polygon fill="grey" stroke="grey" stroke-width="2" points="64.5,-910.1 61,-900.1 57.5,-910.1 64.5,-910.1"/>
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<!-- 12 -->
<g id="node13" class="node">
<title>12</title>
<path fill="none" stroke="#c6d856" stroke-width="2" d="M84.5,-1044C84.5,-1044 37.5,-1044 37.5,-1044 31.5,-1044 25.5,-1038 25.5,-1032 25.5,-1032 25.5,-1020 25.5,-1020 25.5,-1014 31.5,-1008 37.5,-1008 37.5,-1008 84.5,-1008 84.5,-1008 90.5,-1008 96.5,-1014 96.5,-1020 96.5,-1020 96.5,-1032 96.5,-1032 96.5,-1038 90.5,-1044 84.5,-1044"/>
<text text-anchor="middle" x="61" y="-1023.5" font-family="sans" font-size="10.00">ApplyBQSR</text>
</g>
<!-- 12&#45;&gt;11 -->
<g id="edge16" class="edge">
<title>12&#45;&gt;11</title>
<path fill="none" stroke="grey" stroke-width="2" d="M61,-1007.7C61,-999.98 61,-990.71 61,-982.11"/>
<polygon fill="grey" stroke="grey" stroke-width="2" points="64.5,-982.1 61,-972.1 57.5,-982.1 64.5,-982.1"/>
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<!-- 13 -->
<g id="node14" class="node">
<title>13</title>
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<text text-anchor="middle" x="61" y="-1095.5" font-family="sans" font-size="10.00">GatherBQSRReports</text>
</g>
<!-- 13&#45;&gt;12 -->
<g id="edge17" class="edge">
<title>13&#45;&gt;12</title>
<path fill="none" stroke="grey" stroke-width="2" d="M61,-1079.7C61,-1071.98 61,-1062.71 61,-1054.11"/>
<polygon fill="grey" stroke="grey" stroke-width="2" points="64.5,-1054.1 61,-1044.1 57.5,-1054.1 64.5,-1054.1"/>
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<!-- 14 -->
<g id="node15" class="node">
<title>14</title>
<path fill="none" stroke="#56d8c9" stroke-width="2" d="M99,-1188C99,-1188 23,-1188 23,-1188 17,-1188 11,-1182 11,-1176 11,-1176 11,-1164 11,-1164 11,-1158 17,-1152 23,-1152 23,-1152 99,-1152 99,-1152 105,-1152 111,-1158 111,-1164 111,-1164 111,-1176 111,-1176 111,-1182 105,-1188 99,-1188"/>
<text text-anchor="middle" x="61" y="-1173" font-family="sans" font-size="10.00">BaseRecalibrator</text>
<text text-anchor="middle" x="61" y="-1162" font-family="sans" font-size="10.00">patient: A9GRM7</text>
</g>
<!-- 14&#45;&gt;13 -->
<g id="edge18" class="edge">
<title>14&#45;&gt;13</title>
<path fill="none" stroke="grey" stroke-width="2" d="M61,-1151.7C61,-1143.98 61,-1134.71 61,-1126.11"/>
<polygon fill="grey" stroke="grey" stroke-width="2" points="64.5,-1126.1 61,-1116.1 57.5,-1126.1 64.5,-1126.1"/>
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<!-- 15&#45;&gt;9 -->
<g id="edge14" class="edge">
<title>15&#45;&gt;9</title>
<path fill="none" stroke="grey" stroke-width="2" d="M94.84,-791.7C91.09,-783.73 86.55,-774.1 82.38,-765.26"/>
<polygon fill="grey" stroke="grey" stroke-width="2" points="85.49,-763.66 78.06,-756.1 79.16,-766.64 85.49,-763.66"/>
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<!-- 16 -->
<g id="node17" class="node">
<title>16</title>
<path fill="none" stroke="#56d8a9" stroke-width="2" d="M265,-684C265,-684 163,-684 163,-684 157,-684 151,-678 151,-672 151,-672 151,-660 151,-660 151,-654 157,-648 163,-648 163,-648 265,-648 265,-648 271,-648 277,-654 277,-660 277,-660 277,-672 277,-672 277,-678 271,-684 265,-684"/>
<text text-anchor="middle" x="214" y="-663.5" font-family="sans" font-size="10.00">MergeHaplotypeCaller</text>
</g>
<!-- 16&#45;&gt;7 -->
<g id="edge11" class="edge">
<title>16&#45;&gt;7</title>
<path fill="none" stroke="grey" stroke-width="2" d="M196.2,-647.7C187.4,-639.14 176.62,-628.66 167,-619.3"/>
<polygon fill="grey" stroke="grey" stroke-width="2" points="169.2,-616.57 159.59,-612.1 164.32,-621.58 169.2,-616.57"/>
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<!-- 17 -->
<g id="node18" class="node">
<title>17</title>
<path fill="none" stroke="#8fd856" stroke-width="2" d="M249.5,-756C249.5,-756 178.5,-756 178.5,-756 172.5,-756 166.5,-750 166.5,-744 166.5,-744 166.5,-732 166.5,-732 166.5,-726 172.5,-720 178.5,-720 178.5,-720 249.5,-720 249.5,-720 255.5,-720 261.5,-726 261.5,-732 261.5,-732 261.5,-744 261.5,-744 261.5,-750 255.5,-756 249.5,-756"/>
<text text-anchor="middle" x="214" y="-735.5" font-family="sans" font-size="10.00">HaplotypeCaller</text>
</g>
<!-- 17&#45;&gt;16 -->
<g id="edge20" class="edge">
<title>17&#45;&gt;16</title>
<path fill="none" stroke="grey" stroke-width="2" d="M214,-719.7C214,-711.98 214,-702.71 214,-694.11"/>
<polygon fill="grey" stroke="grey" stroke-width="2" points="217.5,-694.1 214,-684.1 210.5,-694.1 217.5,-694.1"/>
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<!-- 18 -->
<g id="node19" class="node">
<title>18</title>
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<text text-anchor="middle" x="217" y="-879.5" font-family="sans" font-size="10.00">SortBam</text>
</g>
<!-- 18&#45;&gt;17 -->
<g id="edge21" class="edge">
<title>18&#45;&gt;17</title>
<path fill="none" stroke="grey" stroke-width="2" d="M215.78,-863.82C215.11,-853.46 214.34,-839.98 214,-828 213.41,-807.28 213.44,-783.83 213.6,-766.21"/>
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<!-- 23 -->
<g id="node24" class="node">
<title>23</title>
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<text text-anchor="middle" x="256" y="-807.5" font-family="sans" font-size="10.00">IndexBam</text>
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<!-- 18&#45;&gt;23 -->
<g id="edge27" class="edge">
<title>18&#45;&gt;23</title>
<path fill="none" stroke="grey" stroke-width="2" d="M226.64,-863.7C231.13,-855.64 236.56,-845.89 241.52,-836.98"/>
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<!-- 19 -->
<g id="node20" class="node">
<title>19</title>
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<!-- 19&#45;&gt;18 -->
<g id="edge23" class="edge">
<title>19&#45;&gt;18</title>
<path fill="none" stroke="grey" stroke-width="2" d="M217,-935.7C217,-927.98 217,-918.71 217,-910.11"/>
<polygon fill="grey" stroke="grey" stroke-width="2" points="220.5,-910.1 217,-900.1 213.5,-910.1 220.5,-910.1"/>
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<!-- 20 -->
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