Changes

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).  

== '''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 first try the other program [http://genome.sph.umich.edu/wiki/Polymutt Polymutt] we developed.  ==

== '''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 first try our sister program [http://genome.sph.umich.edu/wiki/Polymutt Polymutt] .  ==

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