Scipediacontent: Scipediacontent moved page Draft Content 517962082 to Cornish Guda 2015a

2021-02-15T09:51:45Z

Scipediacontent moved page Draft Content 517962082 to Cornish Guda 2015a

Scipediacontent: Created page with " == Abstract == High-throughput sequencing, especially of exomes, is a popular diagnostic tool, but it is difficult to determine which tools are the best at analyzing this da..."

2021-02-15T09:51:41Z

Created page with " == Abstract == High-throughput sequencing, especially of exomes, is a popular diagnostic tool, but it is difficult to determine which tools are the best at analyzing this da..."

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== Abstract ==

High-throughput sequencing, especially of exomes, is a popular diagnostic tool, but it is difficult to determine which tools are the best at analyzing this data. In this study, we use the NIST Genome in a Bottle results as a novel resource for validation of our exome analysis pipeline. We use six different aligners and five different variant callers to determine which pipeline, of the 30 total, performs the best on a human exome that was used to help generate the list of variants detected by the Genome in a Bottle Consortium. Of these 30 pipelines, we found that Novoalign in conjunction with GATK UnifiedGenotyper exhibited the highest sensitivity while maintaining a low number of false positives for SNVs. However, it is apparent that indels are still difficult for any pipeline to handle with none of the tools achieving an average sensitivity higher than 33% or a Positive Predictive Value (PPV) higher than 53%. Lastly, as expected, it was found that aligners can play as vital a role in variant detection as variant callers themselves.

Document type: Article

== Full document ==
<pdf>Media:Draft_Content_517962082-beopen812-5195-document.pdf</pdf>

== Original document ==

The different versions of the original document can be found in:

* [http://downloads.hindawi.com/journals/bmri/2015/456479.pdf http://downloads.hindawi.com/journals/bmri/2015/456479.pdf] under the license https://creativecommons.org/licenses/by

* [http://dx.doi.org/10.1155/2015/456479 http://dx.doi.org/10.1155/2015/456479] under the license cc-by

* [http://europepmc.org/articles/PMC4619817 http://europepmc.org/articles/PMC4619817] under the license http://creativecommons.org/licenses/by/3.0

* [https://dx.doi.org/10.1155/2015/456479 https://dx.doi.org/10.1155/2015/456479]

* [http://downloads.hindawi.com/journals/bmri/2015/456479.pdf http://downloads.hindawi.com/journals/bmri/2015/456479.pdf],
: [http://downloads.hindawi.com/journals/bmri/2015/456479.xml http://downloads.hindawi.com/journals/bmri/2015/456479.xml],
: [http://dx.doi.org/10.1155/2015/456479 http://dx.doi.org/10.1155/2015/456479]

* [http://dx.doi.org/10.1155/2015/456479 http://dx.doi.org/10.1155/2015/456479],
: [https://doaj.org/toc/2314-6133 https://doaj.org/toc/2314-6133],
: [https://doaj.org/toc/2314-6141 https://doaj.org/toc/2314-6141] under the license http://creativecommons.org/licenses/by/3.0/

* [https://www.hindawi.com/journals/bmri/2015/456479 https://www.hindawi.com/journals/bmri/2015/456479],
: [http://downloads.hindawi.com/journals/bmri/2015/456479.pdf http://downloads.hindawi.com/journals/bmri/2015/456479.pdf],
: [https://www.ncbi.nlm.nih.gov/pubmed/26539496 https://www.ncbi.nlm.nih.gov/pubmed/26539496],
: [http://europepmc.org/abstract/MED/26539496 http://europepmc.org/abstract/MED/26539496],
: [https://experts.nebraska.edu/en/publications/a-comparison-of-variant-calling-pipelines-using-genome-in-a-bottl https://experts.nebraska.edu/en/publications/a-comparison-of-variant-calling-pipelines-using-genome-in-a-bottl],
: [https://nebraska.pure.elsevier.com/en/publications/a-comparison-of-variant-calling-pipelines-using-genome-in-a-bottl https://nebraska.pure.elsevier.com/en/publications/a-comparison-of-variant-calling-pipelines-using-genome-in-a-bottl],
: [https://core.ac.uk/display/90670730 https://core.ac.uk/display/90670730],
: [https://academic.microsoft.com/#/detail/2158336776 https://academic.microsoft.com/#/detail/2158336776]

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Cornish Guda 2015a - Revision history

Scipediacontent: Scipediacontent moved page Draft Content 517962082 to Cornish Guda 2015a

Scipediacontent: Created page with " == Abstract == High-throughput sequencing, especially of exomes, is a popular diagnostic tool, but it is difficult to determine which tools are the best at analyzing this da..."