Key features distinguishing the Microhaplotype Caller method:
- The long variant detection responsible for calling MNVs, replacements, and indels in the Low Frequency Variant Detection tool, has been adapted to also call longer more general haplotypes. This enables high resolution allele detection, so multiple haplotype alleles may be distinguished per allele variant and reported with detailed annotations.
- Detected alleles are reported in a locus based representation, making genotypes readily available, e.g. for VCF export.
- When filters are applied, the affected alleles are retained for easy user inspection.
- Forced variant loci can be specified to allow detection of alleles at any site, also homozygous reference loci.
The current version of the Microhaplotype Caller has certain limitations:
- If phasing regions become too large the workbench may run out of memory. Caution must therefore be taken when increasing the 'Maximum phasing distance' parameter from the default value (see Options).
- There is not yet any special homopolymer handling, so length variation artifacts must be considered when analysing loci around longer homopolymers.