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Application data

Created by Manuel A. Rivas and Mark J. Daly
Biological application domain(s) SNP detection, Indel detection
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


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.



  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

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