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Recommendations for performance optimizations when using GATK3.8 and GATK4

Jacob R Heldenbrand, Saurabh Baheti, Matthew A Bockol, Travis M Drucker, Steven N Hart, Matthew E Hudson, Ravishankar K Iyer, Michael T Kalmbach, Katherine I Kendig, Eric W Klee, Nathan R Mattson, Eric D Wieben (+3 others)
2019 BMC Bioinformatics  
We found optimized parameter values that reduce the time of executing the best practices variant calling procedure by 29.3% for GATK3.8 and 16.9% for GATK4.  ...  In such cases we recommend using GATK3.8 by splitting the sample into chunks and computing across multiple nodes.  ...  Neil Cohen at Interdisciplinary Health Sciences Institute, as well as the UIUC Institute for Genomic Biology and the National Center for Supercomputing Applications for their generous support and access  ... 
doi:10.1186/s12859-019-3169-7 pmid:31703611 pmcid:PMC6842142 fatcat:6ztcuz7iavcyragi7d2aaijqua

Performance benchmarking of GATK3.8 and GATK4 [article]

Jacob R Heldenbrand, Saurabh Baheti, Matthew A Bockol, Travis M Drucker, Steven N Hart, Matthew E Hudson, Ravishankar K Iyer, Michael T Kalmbach, Eric W Klee, Eric D Wieben, Mathieu Wiepert, Derek E Wildman (+1 others)
2018 bioRxiv   pre-print
Based on our results, we consider the performance and cost trade-offs of using GATK3.8 and GATK4 for different types of analyses.  ...  Significant computational performance improvements have been introduced in GATK3.8 through collaboration with Intel in 2017.  ...  Major funding was provided by the Mayo Clinic Center for Individualized Medicine and the Todd and Karen Wanek Program for Hypoplastic Left Heart Syndrome.  ... 
doi:10.1101/348565 fatcat:ec44s3e425cnrhgnyfeijbigte

Sentieon DNASeq Variant Calling Workflow Demonstrates Strong Computational Performance and Accuracy

Katherine I. Kendig, Saurabh Baheti, Matthew A. Bockol, Travis M. Drucker, Steven N. Hart, Jacob R. Heldenbrand, Mikel Hernaez, Matthew E. Hudson, Michael T. Kalmbach, Eric W. Klee, Nathan R. Mattson, Christian A. Ross (+5 others)
2019 Frontiers in Genetics  
Our results support the near-identical accuracy of the two software packages, showcase optimal scalability and great speed from Sentieon, and describe computational performance considerations for the deployment  ...  As reliable, efficient genome sequencing becomes ubiquitous, the need for similarly reliable and efficient variant calling becomes increasingly important.  ...  Woese Institute for Genomic Biology and the National Center for Supercomputing Applications for their generous support and access to resources.  ... 
doi:10.3389/fgene.2019.00736 pmid:31481971 pmcid:PMC6710408 fatcat:kinclvsy6reqpgq5lcxwtysvoe

Computational performance and accuracy of Sentieon DNASeq variant calling workflow [article]

Katherine Kendig, Saurabh Baheti, Matthew A Bockol, Travis M Drucker, Steven N Hart, Jacob R Heldenbrand, Mikel Hernaez, Matthew E Hudson, Michael T Kalmbach, Eric W Klee, Nathan R Mattson, Christian A Ross (+5 others)
2018 bioRxiv   pre-print
Our results confirm the near-identical accuracy of the two software packages, showcase perfect scalability and great speed from Sentieon, and describe computational performance considerations for the deployment  ...  As reliable, efficient genome sequencing becomes more ubiquitous, the need for similarly reliable and efficient variant calling becomes increasingly important.  ...  Major funding was provided by the Mayo Clinic Center for Individualized Medicine and the Todd and Karen Wanek Program for Hypoplastic Left Heart Syndrome.  ... 
doi:10.1101/396325 fatcat:qtp3srje2be45fii3azybkeecy

Workstation benchmark of Spark Capable Genome Analysis ToolKit 4 Variant Calling [article]

Marcus H Hansen, Anita T Simonsen, Hans B Ommen, Charlotte G Nyvold
2020 bioRxiv   pre-print
In conclusion, GATK4 offers practical parallelization possibilities for DNA sequence processing, and the Spark-enabled tools optimize performance and utilization of local CPUs.  ...  Compared to the previous GATK version the performance of Spark-enabled BQSR and HaplotypeCaller is shifted towards a more efficient usage of the available cores on CPU and outperforms the earlier GATK3.8  ...  We also wish to thank professor Peter Hokland, Aarhus University Hospital, for continuous scientific supervision and support. .  ... 
doi:10.1101/2020.05.17.101105 fatcat:sqslyzwp65ej7l3egx4bebfuba