Pisces Tools 5.2.10 - Illumina/Pisces GitHub Wiki

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.