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=== Download with example datasets ===
=== Download with example datasets ===
TrioCaller can be downloaded from [http://www.sph.umich.edu/csg/weich/TrioCaller-2012-02-14.tar.gz TrioCaller-2012-02-14.tar.gz].
TrioCaller can be downloaded from here: [http://www.sph.umich.edu/csg/weich/TrioCaller-2012-02-14.tar.gz TrioCaller-2012-02-14.tar.gz].
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.
The average sequence depth is ~3x.
The average sequence depth is ~3x. README.txt describes the structure of the package. Pipeline.csh (C shell) and pipeline.bash (bash shell) are two scripts for you to run all commands listed here in batch.
To conserve time and disk-space, our analysis will focus on a small region on chromosome 20 around position 2,000,000. We will first map reads for a single individual (labeled SAMPLE1). Then we combine the results with mapped reads from all individuals to generate a list of polymorphic sites and estimate accurate genotypes at each of these sites.
To conserve time and disk-space, our analysis will focus on a small region on chromosome 20 around position 2,000,000. We will first map reads for a single individual (labeled SAMPLE1). Then we combine the results with mapped reads from all individuals to generate a list of polymorphic sites and estimate accurate genotypes at each of these sites.
