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, 00:20, 13 May 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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− | '''Note:''' 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.
| + | === Polymutt === |
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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. |
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| === Download === | | === Download === |