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 detection of low frequency variants, such as those found in heterogeneous cancer 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 www.illumina.com/documents/products/technotes/technote_somatic_variant_caller.pdf.