The program is a resequencing ulity that can assemble

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Unformatted text preview: may not work well in samples with higher ploidy. 31 SNP Calling SoIware Packages •  GATK (The Genome Analysis Toolkit) a set of tools, which include coverage analyzers, a quality score recalibrator, and a SNP/indel caller. –  Developed at the Broad Ins/tute. –  Used in human medical resequencing projects such as 1000 Genomes and The Cancer Genome Atlas. –  Greatest accuracy; most complicated to use. 32 33 SNP Calling SoIware Packages •  MAQ (Mapping and Assembly with Quality) builds assembly by mapping short reads to reference sequences. –  Mainly used for SNP ­calling but also does alignment of reads. –  Developed at the University of Cambridge. –  Produces a non ­standard formafed file that has to be converted into a SA...
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This note was uploaded on 02/10/2014 for the course CS 680 taught by Professor Staff during the Fall '08 term at Colorado State.

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