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--minDepth ''threshold'' Positions where the read depth falls below this threshold will be excluded.
--minDepth ''threshold'' Positions where the read depth falls below this threshold will be excluded.
--maxDepth ''threshold'' Positions where the read depth exceeds this threshold will be excluded.
--maxDepth ''threshold'' Positions where the read depth exceeds this threshold will be excluded.
--hardFilter Filtered positions will be completely absent from output. The default is to use a soft filter, where these
positions are included in output but annotated as failing specific filters.
=== VCF Output ===
=== VCF Output ===
to be matched to a more specific individual identifier. The aliases file should include two columns per row,
to be matched to a more specific individual identifier. The aliases file should include two columns per row,
the first specifying the VCF filename, the second specifying a sample name.
the first specifying the VCF filename, the second specifying a sample name.
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=== X Chromosome Variant Calling ===
=== X Chromosome Variant Calling ===
--xStop ''sexChromosomeEnd'' End of the non-pseudo-autosomal portion of the X (154,584,237 bp in build 36)
--xStop ''sexChromosomeEnd'' End of the non-pseudo-autosomal portion of the X (154,584,237 bp in build 36)
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== How It Works ==
For each possible position, glfMultiples considers a series of potential polymorphisms, including transitions and transversions from the reference base, but also bi-allelic polymorphisms where neither of the alleles present in the sample is the reference base. For each potential polymorphism type, the likelihood of the observed bases is maximized with respect to allele frequency. Decisions of which sites are polymorphic take into account the maximized likelihood but also an overall prior for each type of polymorphism (for example, transitions are assumed to account for ~2/3 of all variants).
glfMultiples works with log-likelihoods internally to avoid underflows in samples that may include hundreds or thousands of individuals.
== Download ==
== Download ==
The current version is available for download from [http://www.sph.umich.edu/csg/abecasis/downloads/generic-glfMultiples-2010-05-20.tar.gz here].
The current version is available for download from http://www.sph.umich.edu/csg/abecasis/downloads/generic-glfMultiples-2010-06-16.tar.gz.
== TODO ==
== TODO ==
