Analysis Methods | Isaac Variant Caller | Variant Call Output

Variant Call Output

After the SNV and indel genotyping methods are complete, the variant caller applies a final set of heuristic filters to produce the final set of calls in the output.

The output in the genome variant call (gVCF) file captures the genotype at each position and the probability that the consensus call differs from reference. This score is expressed as a Phred-scaled quality score.