Pisces Tools 5.2.10
tamsen edited this page Feb 20, 2019
·
1 revision
The following helpful tools are provided as-is to the community. Type "dotnet [application].dll -h" to see the available options.
- Hygea : Unstable, made obsolete be Gemini
- VennVcf : Simple tool to take in two vcfs and get the intersection, disjoint sets, and consensus vcf (pooling the depths and recalling).
- CreateGenomeSizeFile : Creates the "GenomeSize.xml" file for a given genome (.fa). Useful if you want to use Pisces for custom genomes.
- AdaptiveGenotyper : Re-genotypes a given vcf with a more sophisticated model than Pisces's original threshold-based diploid model. Given a vcf from a germline sample, which has been called in somatic, uncrushed VCF mode (in order to report all alleles present, including noise), AdaptiveGenotyper will then adaptively build up three-component (or four-component) binomial mixture models as appropriate for a diploid sample, and re-genotype based on those models.
- Pisces 5.2.10 Design Document
- Pisces 5.2.10 Supported Options
- Scylla 5.2.10 Design Document
- Stitcher 5.2.10 Design Document
- VQR 5.2.10 Design Document
- VennVcf 5.2.10 Design Document
- Gemini 5.2.10 Design Document
- AdaptiveGenotyper 5.2.10 Design Document
- Pisces Tools 5.2.10
- Suggested Pipeline Configuration 5.2.10
- Pisces 5.2.9 Quick Start
- Pisces 5.2.9 Design Document
- Pisces 5.2.9 Supported Options
- Scylla 5.2.9 Design Document
- Stitcher 5.2.9 Design Document
- VQR 5.2.9 Design Document
- VennVcf 5.2.9 Design Document
- Pisces Tools 5.2.9
- Suggested Pipeline Configuration 5.2.9
- Pisces 5.2.7 Quick Start
- Pisces 5.2.7 Design Document
- Pisces 5.2.7 Supported Options
- Scylla 5.2.7 Design Document
- Stitcher 5.2.7 Design Document
- VQR 5.2.7 Design Document
- VennVcf 5.2.7 Design Document
- Pisces Tools 5.2.7
- Suggested Pipeline Configuration 5.2.7
- Pisces 5.2.5 Design Document
- Pisces 5.2.5 Supported Options
- Scylla 5.2.5 Design Document
- Stitcher 5.2.5 Design Document
- VQR 5.2.5 Design Document
- Suggested Pipeline Configuration 5.2.5
- Pisces 5.2.0 Design Document
- Pisces 5.2.0 Supported Options
- Scylla 5.2.0 Design Document
- Stitcher 5.2.0 Design Document
- VQR 5.2.0 Design Document
- Suggested Pipeline Configuration 5.2.0
- Pisces Suite 5.2.0 Known Issues and Limitations