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, 12:28, 4 December 2013
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| We will start with a set of short sequence reads and associated base quality scores (stored in a fastq file), find the most likely genomic location for each read (producing a BAM file), generate an initial list of polymorphic sites and genotypes (stored in a VCF file) and use haplotype information to refine these genotypes (resulting in an updated VCF file). | | We will start with a set of short sequence reads and associated base quality scores (stored in a fastq file), find the most likely genomic location for each read (producing a BAM file), generate an initial list of polymorphic sites and genotypes (stored in a VCF file) and use haplotype information to refine these genotypes (resulting in an updated VCF file). |
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− | === Polymutt === | + | === Note === |
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− | If you are interested in ''de novo'' mutations or are working on families with deep sequence data, you should also consider our sister program, [http://genome.sph.umich.edu/wiki/Polymutt Polymutt], which ignores linkage disequilibrium information but can handle more complex pedigrees. | + | If you are interested in ''de novo'' mutations or are working on one or two families with deep sequence data (>30X), you should first consider our sister program, [http://genome.sph.umich.edu/wiki/Polymutt Polymutt], which ignores linkage disequilibrium information but can handle more complex pedigrees. |
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| === Download === | | === Download === |