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, 15:17, 23 September 2013
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| == Model for Variant Calling == | | == Model for Variant Calling == |
| + | glfSingle uses a likelihood-based model for variant calling. Starting from genotype likelihoods ''Pr(reads| genotype)'' per genomic position, computed from appropriate tools (eg. Samtools BAQ), the likelihoods combine with an individual-based prior ''p(genotype)'' to generate posterior probabilities ''Pr(genotype| reads)''. |
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| + | Ingredients that go into prior: |
| + | *All sites have an equal probability of showing polymorphism: |
| + | **P(non-reference base) = 0.001 |
| + | *When a site shows polymorphism, it is usually heterozygous: |
| + | **P(non-reference heterozygote) = 0.01 * 2/3 |
| + | **P(non-reference homozygote) = 0.01 * 1/3 |
| + | *Two options of mutation model: |
| + | **Transitions (C <-> T or A <-> G) accounts for most variants, while transversions account for minority of variants |
| + | **Uniform prior for transition to transversion ratio (1:1) |
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| == Download == | | == Download == |