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, 18:43, 17 February 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 interesting in detecting '''de novo mutations''', or are working on a small number of families with high coverage data (e.g. exome sequencing), | + | '''Note:''' if you are interesting in detecting '''de novo mutations''', or are working on '''a small number of families''' with '''high coverage data''' (e.g. exome sequencing), |
− | please try the other program [http://genome.sph.umich.edu/wiki/Polymutt Polymutt] we developed. | + | please first try the other program [http://genome.sph.umich.edu/wiki/Polymutt Polymutt] we developed. |
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| === Download === | | === Download === |