Syzygy

From SEQwiki
Jump to: navigation, search

Application data

Created by Manuel A. Rivas and Mark J. Daly
Biological application domain(s) SNP discovery, InDel discovery
Created at Broad Institute
Maintained? Yes
Input format(s) BAM
Output format(s) Various
Programming language(s) Python, R

Summary: Software to identify variants from pooled sequencing data

Description

Syzygy is a targeted sequencing post processing analysis tool that allows:

Rare variant SNP detection; Allele frequency estimation; Single-marker association test; Group-wise marker test association; Experimental QC summary (%dbSNP, Ts/Tv, Ns/S); Power to detect variant.

Documentation seems to indicate that Syzygy works for either indexed/barcoded or non-indexed (where individual-of-origin is not known for reads) pooled samples.






Links


References

  1. Calvo SE, Tucker EJ, Compton AG, Kirby DM, Crawford G, Burtt NP, Rivas M, Guiducci C, Bruno DL, Goldberger OA, Redman MC, Wiltshire E, Wilson CJ, Altshuler D, Gabriel SB, Daly MJ, Thorburn DR, Mootha VK.. 2010. Nature Genetics
  2. Rivas, M.A., et al. 2011. Nature Genetics


To add a reference for Syzygy, enter the PubMed ID in the field below and click 'Add'.


[ edit box ]

Search for "Syzygy" in the SEQanswers forum / BioStar or:

Web Search Wiki Sites Scientific
Personal tools
Namespaces

Variants
Actions
wiki navigation
Software
Toolbox