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== Introduction ==
== Introduction ==
We will illustrate how TrioCaller works in sequence data including trios and unrelated samples. We will start from the scratch and walk through all necessary steps from raw sequence data to called genotypes. If you are new to sequence data, please be patient to go through every step. If you are experienced, you may directly jump to the section of [http://genome.sph.umich.edu/wiki/TrioCaller#Genotype_Refinement_Using_Linkage_Disequilibrium_Information_.28TrioCaller.29 TrioCaller].
We will illustrate how TrioCaller works in sequence data including trios and unrelated samples. We will walk through all necessary steps to move from raw sequence data to called genotypes.
If you are new to sequence data, please review every step. If you are experienced, you may directly jump to [http://genome.sph.umich.edu/wiki/TrioCaller#Genotype_Refinement_Using_Linkage_Disequilibrium_Information_.28TrioCaller.29 TrioCaller] specific section.
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 our sister program [http://genome.sph.umich.edu/wiki/Polymutt Polymutt] . ==
== '''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] . ==
