It throws warnings when substantial charges of Mendel faults are detected at the family members or web site amount and generates 2 log information to easily location any complications:
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SHAPEIT is a fast and correct process for estimation of haplotypes (aka phasing) from genotype or sequencing knowledge.
This can be a default binary file structure employed by Plink. This format is incredibly handy for large datasets as it needs very low HDD memory usage. You'll find a specific description on the Plink binary format in this article.
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Supplies the haplotype graph for every individual within the sample when the phasing system accomplished. Might be read with SHAPEIT when using the -convert mode. Additional details about this options right here and here.
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Monomorphic web pages in PLINK Mattress format information don't now contain the alternate allele coded as 0, which means some incompatibility with Impute2.
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famID: An distinctive id internally assigned by SHAPEIT to every distinctive family members (useful to ascertain the quantity of unrelated family members there are actually).
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