Variant Calling

SNPs and short indels are identified using the Somatic Variant Caller. Developed by Illumina, the Somatic Variant Caller identifies variants present at low frequency in the DNA sample and minimizes false positives.

The Somatic Variant Caller identifies SNPs in 3 steps:

} Considers each position in the reference genome separately.
} Counts bases at the given position for aligned reads that overlap the position.
} Computes a variant score that measures the quality of the call.

Variant scores are computed using a Poisson model that excludes variants with a variant quality score below Q20. The model only calls variants for bases that are covered at 300x or greater for a single amplicon.

Variants are first called for each pool separately. Then, variants from the 2 pools are compared and combined into a single output file.

If a variant meets the following criteria, the variant is marked as PASS in the variant file:

} Present in both pools.
} Cumulative depth of 1000 or average depth of 500x per pool.
} Meets all the VCF filter requirements as specified. See VCF Entries.

For more information, see the Amplicon - DS Variant Caller Technical Note on the TruSight Tumor 26 support page.

 

© 2015 Illumina, Inc. All rights reserved.

Document # 15066595 v02