Germline Variant Caller

Developed by Illumina, the germline variant caller identifies variants in DNA samples.

The germline variant caller genotypes candidate variants according to a set of configurable thresholds:

•

Variants below 20% variant frequency are discarded.

•

SNVs with frequencies between 20% and 90% and indels with frequencies between 20% and 70% are classified as heterozygous (0/1 genotype).

•

SNVs with frequencies above 90% and indels with frequencies above 70% are classified as homozygous alternative variants (1/1 genotype).

•

When multiple candidate variants are identified at the same locus, the caller attempts to merge these variants into a diploid-conform variant. The merging is not performed when genotypes of interest VCF files are provided.

A candidate variant is filtered under the following conditions:

•

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

•

The variant quality is below Q20.

•

Significant strand bias is detected.

•

The variant occurs in a repetitive region.

•

The variant does not conform to the diploid model.

•

The no-call rate is above 0.6.