Somatic Variant Caller

Developed by Illumina, the somatic variant caller identifies variants present at low frequency in DNA samples.

The somatic variant caller identifies variants in three steps:

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Considers each position in the reference genome separately.

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Counts bases at a given position for aligned reads that overlap the position.

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Computes a variant score that measures the quality of the call using a Poisson model.

A candidate variant is filtered under the following conditions:

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The frequency is below the user-specified threshold (default: 5%).

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The depth is below the user-specified threshold (default: 10).

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The variant quality is below Q30.

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Significant strand bias is detected.

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The variant occurs in a repetitive region.

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The no-call rate is above 0.6.