Analysis Methods | Isaac Variant Caller

Isaac Variant Caller

The Isaac variant caller identifies single nucleotide variants (SNVs) and small indels using the following steps:

Read filtering—Filters reads failing quality checks.
Indel calling—Identifies a set of possible indel candidates and realigns all reads overlapping the candidates using a multiple sequence aligner.
SNV calling—Computes the probability of each possible genotype given the aligned read data and a prior distribution of variation in the genome.
Indel genotypes—Calls indel genotypes and assigns probabilities.
Variant call output—Generates output in a VCF and a compressed genome variant call (gVCF) file.

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