Somatic Variant Caller

The Somatic Variant Caller is designed for variant calling in tumor samples with no paired normal. The Somatic Variant Caller is recommended for TruSeq Amplicon - Cancer Panel and TruSight Myeloid Sequencing Panel samples.

Variants are flagged as homozygous or heterozygous in the VCF sample column, with either a 1/1 or a 0/1 respectively. During somatic variant calling, somatic variants are observed at any frequency. Therefore, het/hom calls are made to indicate the most reasonable diploid genotype that can be assigned to a variant if it is a non-somatic (germline) variant.

For more information about the Somatic Variant Caller, see res.illumina.com/documents/products/technotes/technote_somatic_variant_caller.pdf.