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The initial set of genotype calls is generated examining a single individual at a time. These calls are typically quite good for deep sequencing data, but much less accurate for low pass sequence data. In either case, they can be greatly improved by models that combine information across sites and individuals and consider the contraints imposed by parent-offspring trios.
The initial set of genotype calls is generated examining a single individual at a time. These calls are typically quite good for deep sequencing data, but much less accurate for low pass sequence data. In either case, they can be greatly improved by models that combine information across sites and individuals and consider the contraints imposed by parent-offspring trios.
Here is a summary of the FamLDCaller command line options (these are also listed whenever you run the program with no parameters):
Here is a summary of the TrioCaller command line options (these are also listed whenever you run the program with no parameters):
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Note: The pedigree files require complete trio structures (all three members of the trio exist in the file). For parent-offspring pair, create a "fake" parent in the pedigree file or code them as unrelated individuals. The order of the names in the pedigree file is NOT necessary to be consistent with that in .vcf file. The computation will be intensive if the number of samples are large.
Note: The pedigree files require complete family structures (both parents must exist in the pedigree file, e.g. for parent-offspring pair, create a "fake" parent in the pedigree file or code them as unrelated individuals). The order of the names in the pedigree file is NOT necessary to be consistent with that in .vcf file. The computation will be intensive if the number of samples are large.
You can use option "--states" to reduce the computation cost (e.g. start with "--states 50")
You can use option "--states" to reduce the computation cost (e.g. start with "--states 50")
