Difference between revisions of "Utah Genome Project"
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* [http://srynobio.github.io/cApTUrE cApTUrE] - a lightweight NGS analysis pipeline implementing the UGP variant calling protocol) | * [http://srynobio.github.io/cApTUrE cApTUrE] - a lightweight NGS analysis pipeline implementing the UGP variant calling protocol) | ||
* The [http://healthcare.utah.edu/huntsmancancerinstitute/research/shared-resources/center-managed/bioinformatics/ HCI Informatics] team have created a pipeline using [http://healthcare.utah.edu/huntsmancancerinstitute/research/shared-resources/center-managed/bioinformatics/useful-links/software-tomato2.php Tomato2] that implements the UGP Variant Protocol | * The [http://healthcare.utah.edu/huntsmancancerinstitute/research/shared-resources/center-managed/bioinformatics/ HCI Informatics] team have created a pipeline using [http://healthcare.utah.edu/huntsmancancerinstitute/research/shared-resources/center-managed/bioinformatics/useful-links/software-tomato2.php Tomato2] that implements the UGP Variant Protocol | ||
| − | * [[ | + | |
| + | == Protocol Developement == | ||
| + | |||
| + | The UGP is developing a variant protocol that utilizes the [https://github.com/ekg/freebayes FreeBayes] variant caller from the [http://www.bioscience.utah.edu/faculty/molecular-biology-faculty/marth/ Marth Lab] | ||
| + | * [[UGP_FreeBayes_Variant_Protocol | UGP FreeBayes Variant Protocol]] | ||
Revision as of 05:02, 11 February 2015
The Utah Genome Project has developed a detailed variant calling protocol based on the GATK HapoltypeCaller. This protocol very closely follows the GATK Best Practices for variant calling on DNAseq data, however here we provide detailed and versioned protocol that includes exact command lines for each step in the analysis as well as links to accessory datasets.
UGP Variant Calling
- UGP Variant Calling Protocol
- cApTUrE - a lightweight NGS analysis pipeline implementing the UGP variant calling protocol)
- The HCI Informatics team have created a pipeline using Tomato2 that implements the UGP Variant Protocol
Protocol Developement
The UGP is developing a variant protocol that utilizes the FreeBayes variant caller from the Marth Lab
