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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).
=== Download with example datasets ===
=== Download ===
Binary file only: [http://www.sph.umich.edu/csg/weich/TrioCaller04242012.binary.tgz TrioCaller.04242012.tgz].
Binary file with example datasets : [http://www.sph.umich.edu/csg/weich/TrioCaller04242012.tgz TrioCaller.04242012.tgz].
The example dataset demonstrated here is also included. Our dataset consists of 40 individuals, including 10 parent-offspring trios and 10 unrelated individuals.
The example dataset demonstrated here is also included. Our dataset consists of 40 individuals, including 10 parent-offspring trios and 10 unrelated individuals.
