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<title>References | A practical introduction to GATK 4 on Biowulf (NIH HPC)</title>
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<li><a href="./">GATK on biowulf</a></li>
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<li class="chapter" data-level="" data-path="index.html"><a href="index.html"><i class="fa fa-check"></i>Prerequisites</a>
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<li class="chapter" data-level="" data-path="index.html"><a href="index.html#software"><i class="fa fa-check"></i>Software</a></li>
<li class="chapter" data-level="" data-path="index.html"><a href="index.html#sequencing-data"><i class="fa fa-check"></i>Sequencing data</a></li>
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<li class="chapter" data-level="1" data-path="preproc.html"><a href="preproc.html"><i class="fa fa-check"></i><b>1</b> Data preprocessing</a>
<ul>
<li class="chapter" data-level="1.1" data-path="preproc.html"><a href="preproc.html#brief-introduction"><i class="fa fa-check"></i><b>1.1</b> Brief introduction</a></li>
<li class="chapter" data-level="1.2" data-path="preproc.html"><a href="preproc.html#preproc-tools"><i class="fa fa-check"></i><b>1.2</b> Tools</a></li>
<li class="chapter" data-level="1.3" data-path="preproc.html"><a href="preproc.html#preproc-single-tools"><i class="fa fa-check"></i><b>1.3</b> Individual tool benchmarks</a>
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<li class="chapter" data-level="1.3.1" data-path="preproc.html"><a href="preproc.html#preproc-trim"><i class="fa fa-check"></i><b>1.3.1</b> Adapter trimming</a></li>
<li class="chapter" data-level="1.3.2" data-path="preproc.html"><a href="preproc.html#preproc-align"><i class="fa fa-check"></i><b>1.3.2</b> Alignment</a></li>
<li class="chapter" data-level="1.3.3" data-path="preproc.html"><a href="preproc.html#preproc-sort"><i class="fa fa-check"></i><b>1.3.3</b> Alternative A: Sorting by coordinate</a></li>
<li class="chapter" data-level="1.3.4" data-path="preproc.html"><a href="preproc.html#preproc-view"><i class="fa fa-check"></i><b>1.3.4</b> Alternative B: Queryname-grouped (unsorted) BAM</a></li>
</ul></li>
<li class="chapter" data-level="1.4" data-path="preproc.html"><a href="preproc.html#optimized-script"><i class="fa fa-check"></i><b>1.4</b> Optimized script</a>
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<li class="chapter" data-level="1.4.1" data-path="preproc.html"><a href="preproc.html#alternative-a-producing-sorted-bam-output"><i class="fa fa-check"></i><b>1.4.1</b> Alternative A: producing sorted BAM output</a></li>
<li class="chapter" data-level="1.4.2" data-path="preproc.html"><a href="preproc.html#preproc-nosort-pipeline"><i class="fa fa-check"></i><b>1.4.2</b> Alternative B: BAM output without coordinate sorting</a></li>
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<li class="chapter" data-level="1.5" data-path="preproc.html"><a href="preproc.html#read-groups"><i class="fa fa-check"></i><b>1.5</b> Read groups</a></li>
<li class="chapter" data-level="1.6" data-path="preproc.html"><a href="preproc.html#processing-the-example-trio"><i class="fa fa-check"></i><b>1.6</b> Processing the example trio</a></li>
</ul></li>
<li class="chapter" data-level="2" data-path="workflow-overview.html"><a href="workflow-overview.html"><i class="fa fa-check"></i><b>2</b> GATK practice workflow</a>
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<li class="chapter" data-level="2.1" data-path="workflow-overview.html"><a href="workflow-overview.html#cleaning-up-raw-alignments"><i class="fa fa-check"></i><b>2.1</b> Cleaning up raw alignments</a></li>
<li class="chapter" data-level="2.2" data-path="workflow-overview.html"><a href="workflow-overview.html#joint-calling"><i class="fa fa-check"></i><b>2.2</b> Joint Calling</a></li>
<li class="chapter" data-level="2.3" data-path="workflow-overview.html"><a href="workflow-overview.html#variant-filtering"><i class="fa fa-check"></i><b>2.3</b> Variant filtering</a></li>
</ul></li>
<li class="chapter" data-level="3" data-path="markdup.html"><a href="markdup.html"><i class="fa fa-check"></i><b>3</b> MarkDuplicates</a>
<ul>
<li class="chapter" data-level="3.1" data-path="markdup.html"><a href="markdup.html#brief-introduction-1"><i class="fa fa-check"></i><b>3.1</b> Brief introduction</a></li>
<li class="chapter" data-level="3.2" data-path="markdup.html"><a href="markdup.html#benchmarks-of-markduplicatesspark"><i class="fa fa-check"></i><b>3.2</b> Benchmarks of <code>MarkDuplicatesSpark</code></a>
<ul>
<li class="chapter" data-level="3.2.1" data-path="markdup.html"><a href="markdup.html#queryname-grouped-input-data-as-generated-by-the-aligner"><i class="fa fa-check"></i><b>3.2.1</b> Queryname-grouped input data (as generated by the aligner)</a></li>
<li class="chapter" data-level="3.2.2" data-path="markdup.html"><a href="markdup.html#coordinate-sorted-input-data"><i class="fa fa-check"></i><b>3.2.2</b> Coordinate-sorted input data</a></li>
<li class="chapter" data-level="3.2.3" data-path="markdup.html"><a href="markdup.html#performance-comparing-between-queryname-grouped-and-coordinate-sorted-inputs"><i class="fa fa-check"></i><b>3.2.3</b> Performance comparing between queryname-grouped and coordinate-sorted inputs</a></li>
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<li class="chapter" data-level="3.3" data-path="markdup.html"><a href="markdup.html#optimized-script-1"><i class="fa fa-check"></i><b>3.3</b> Optimized script</a></li>
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<li class="chapter" data-level="4" data-path="bqsr.html"><a href="bqsr.html"><i class="fa fa-check"></i><b>4</b> BQSR</a>
<ul>
<li class="chapter" data-level="4.1" data-path="bqsr.html"><a href="bqsr.html#brief-introduction-2"><i class="fa fa-check"></i><b>4.1</b> Brief introduction</a></li>
<li class="chapter" data-level="4.2" data-path="bqsr.html"><a href="bqsr.html#benchmarks-of-baserecalibrator"><i class="fa fa-check"></i><b>4.2</b> Benchmarks of <code>BaseRecalibrator</code></a></li>
<li class="chapter" data-level="4.3" data-path="bqsr.html"><a href="bqsr.html#optimized-script-for-baserecalibrator"><i class="fa fa-check"></i><b>4.3</b> Optimized script for <code>BaseRecalibrator</code></a></li>
<li class="chapter" data-level="4.4" data-path="bqsr.html"><a href="bqsr.html#benchmarks-of-applybqsr"><i class="fa fa-check"></i><b>4.4</b> Benchmarks of <code>ApplyBQSR</code></a></li>
<li class="chapter" data-level="4.5" data-path="bqsr.html"><a href="bqsr.html#optimized-script-for-applybqsr"><i class="fa fa-check"></i><b>4.5</b> Optimized script for <code>ApplyBQSR</code></a></li>
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<li class="chapter" data-level="5" data-path="haplotype-caller.html"><a href="haplotype-caller.html"><i class="fa fa-check"></i><b>5</b> HaplotypeCaller</a>
<ul>
<li class="chapter" data-level="5.1" data-path="haplotype-caller.html"><a href="haplotype-caller.html#brief-introduction-3"><i class="fa fa-check"></i><b>5.1</b> Brief introduction</a></li>
<li class="chapter" data-level="5.2" data-path="haplotype-caller.html"><a href="haplotype-caller.html#benchmarks"><i class="fa fa-check"></i><b>5.2</b> Benchmarks</a></li>
<li class="chapter" data-level="5.3" data-path="haplotype-caller.html"><a href="haplotype-caller.html#optimized-script-2"><i class="fa fa-check"></i><b>5.3</b> Optimized script</a></li>
</ul></li>
<li class="chapter" data-level="6" data-path="genomics-db-import.html"><a href="genomics-db-import.html"><i class="fa fa-check"></i><b>6</b> GenomicsDBImport (replaces CombineGVCFs)</a>
<ul>
<li class="chapter" data-level="6.1" data-path="genomics-db-import.html"><a href="genomics-db-import.html#brief-introduction-4"><i class="fa fa-check"></i><b>6.1</b> Brief introduction</a></li>
<li class="chapter" data-level="6.2" data-path="genomics-db-import.html"><a href="genomics-db-import.html#benchmarks-1"><i class="fa fa-check"></i><b>6.2</b> Benchmarks</a></li>
<li class="chapter" data-level="6.3" data-path="genomics-db-import.html"><a href="genomics-db-import.html#optimized-script-3"><i class="fa fa-check"></i><b>6.3</b> Optimized script</a></li>
</ul></li>
<li class="chapter" data-level="7" data-path="genotype-gvcfs.html"><a href="genotype-gvcfs.html"><i class="fa fa-check"></i><b>7</b> GenotypeGVCFs</a>
<ul>
<li class="chapter" data-level="7.1" data-path="genotype-gvcfs.html"><a href="genotype-gvcfs.html#brief-introduction-5"><i class="fa fa-check"></i><b>7.1</b> Brief introduction</a></li>
<li class="chapter" data-level="7.2" data-path="genotype-gvcfs.html"><a href="genotype-gvcfs.html#benchmarks-2"><i class="fa fa-check"></i><b>7.2</b> Benchmarks</a></li>
<li class="chapter" data-level="7.3" data-path="genotype-gvcfs.html"><a href="genotype-gvcfs.html#optimized-script-4"><i class="fa fa-check"></i><b>7.3</b> Optimized script</a></li>
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<li class="chapter" data-level="8" data-path="vqsr.html"><a href="vqsr.html"><i class="fa fa-check"></i><b>8</b> VQSR</a>
<ul>
<li class="chapter" data-level="8.1" data-path="vqsr.html"><a href="vqsr.html#brief-introduction-6"><i class="fa fa-check"></i><b>8.1</b> Brief introduction</a></li>
<li class="chapter" data-level="8.2" data-path="vqsr.html"><a href="vqsr.html#benchmarks-of-variantrecalibrator"><i class="fa fa-check"></i><b>8.2</b> Benchmarks of <code>VariantRecalibrator</code></a></li>
<li class="chapter" data-level="8.3" data-path="vqsr.html"><a href="vqsr.html#optimized-script-for-variantrecalibrator"><i class="fa fa-check"></i><b>8.3</b> Optimized script for <code>VariantRecalibrator</code></a></li>
<li class="chapter" data-level="8.4" data-path="vqsr.html"><a href="vqsr.html#benchmarks-of-applyvqsr"><i class="fa fa-check"></i><b>8.4</b> Benchmarks of <code>ApplyVQSR</code></a></li>
<li class="chapter" data-level="8.5" data-path="vqsr.html"><a href="vqsr.html#optimized-script-for-applyvqsr"><i class="fa fa-check"></i><b>8.5</b> Optimized script for <code>ApplyVQSR</code></a></li>
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<li class="chapter" data-level="9" data-path="gt-posteriors.html"><a href="gt-posteriors.html"><i class="fa fa-check"></i><b>9</b> Calculate genotype posteriors</a>
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<li class="chapter" data-level="9.1" data-path="gt-posteriors.html"><a href="gt-posteriors.html#brief-introduction-7"><i class="fa fa-check"></i><b>9.1</b> Brief introduction</a></li>
<li class="chapter" data-level="9.2" data-path="gt-posteriors.html"><a href="gt-posteriors.html#benchmarks-3"><i class="fa fa-check"></i><b>9.2</b> Benchmarks</a></li>
<li class="chapter" data-level="9.3" data-path="gt-posteriors.html"><a href="gt-posteriors.html#optimized-script-5"><i class="fa fa-check"></i><b>9.3</b> Optimized script</a></li>
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Eberle, Michael A., Epameinondas Fritzilas, Peter Krusche, Morten Källberg, Benjamin L. Moore, Mitchell A. Bekritsky, Zamin Iqbal, et al. 2017. <span>“A Reference Data Set of 5.4 Million Phased Human Variants Validated by Genetic Inheritance from Sequencing a Three-Generation 17-Member Pedigree.”</span> <em>Genome Research</em> 27 (1): 157–64. <a href="https://doi.org/10.1101/gr.210500.116">https://doi.org/10.1101/gr.210500.116</a>.
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