Isaac Variant Caller
The Isaac variant caller identifies single nucleotide variants (SNVs) and small indels using the following steps:
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Read filtering—Filters reads failing quality checks. |
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Indel calling—Identifies a set of possible indel candidates and realigns all reads overlapping the candidates using a multiple sequence aligner. |
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SNV calling—Computes the probability of each possible genotype given the aligned read data and a prior distribution of variation in the genome. |
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Indel genotypes—Calls indel genotypes and assigns probabilities. |
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Variant call output—Generates output in a VCF and a compressed genome variant call (gVCF) file. |
For more information, see https://github.com/sequencing/isaac_variant_caller
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