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 three 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. Additionally, 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 two 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:

• Must be present in both pools.
• Cumulatively have a depth of 1000 or an average depth of 500x per pool.
• Meets all the VCF filter requirements as specified. See Amplicon DS VCF Entries.

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

 

© 2014 Illumina, Inc. All rights reserved.

15066595 Rev. B