What is the multi-sample variant caller and how does it work?

This filter is designed to reduce the number of false positive (FP) variant calls and avoid false negatives (FN) in homopolymer regions on IonTorrent platforms. It works by distinguishing systematic errors from the real biological variant signal. The signal is compared across samples, and if a certain pattern is found in every sample it is regarded as a likely systematic error and not real.

This variant caller handles only variants in homopolymers (i.e., variants that change the length of the homopolymer) or small INDELs like single nucleotide insertions or deletions, as such variants are known to be most affected by errors of the IonTorrent platform. This filter does not affect SNPs or other types of INDELs.

IMPORTANT NOTE: The module requires a minimum of 4 samples (minimum 8 recommended). Fewer than 4 samples will not benefit from the multi-sample variant caller, leading to potential differences in the reported variants.

TIP: only samples processed together should be analysed together, as error profiles can be different between runs.