Microhaplotype Caller (beta)

The Microhaplotype Caller (beta) identifies sample alleles at variant loci as well as specified marker loci, uses phasing information available in the mapped reads to infer haplotypes, and produces a Genotype track with all detected alleles, including, for inspection, those not called due to applied filters.

The Microhaplotype Caller (beta) takes advantage of the same probabilistic approach as the Low Frequency Variant Detection tool, it is therefore suitable for analysis of mixed tissue samples in which low frequent variants are likely to be present, as well as for samples for which the ploidy is unknown or not well defined. For method details, see: https://resources.qiagenbioinformatics.com/manuals/clcgenomicsworkbench/current/index.php?manual=_Low_Frequency_Variant_Detection_tool_Models_methods.html

Key features distinguishing the Microhaplotype Caller (beta) method:

The current version of the Microhaplotype Caller (beta) has certain limitations:

To run the Microhaplotype Caller (beta), go to:

        Toolbox | Biomedical Genomics Analysis (Image biomedical_folder_closed_16_n_p) | Haplotype Calling (beta) (Image hac_folder_closed_16_n_p) | Microhaplotype Caller (beta) (Image snp_detection)

The Microhaplotype Caller (beta) has three options to select information available in the output (figure 10.6):

Image options
Figure 10.6: The Microhaplotype Caller options.

General filters

There are three main properties by which the output can be filtered, and each of these have a detection and a call threshold (figure 10.7). The detection threshold specifies if elements are reported or not, whereas the call threshold specifies whether an element is marked with a filter to be disregarded as noise. Elements with applied filters are however still reported for inspection, which can be useful for evaluating borderline calls.

Image filters-general
Figure 10.7: The Microhaplotype Caller general filters.

Detection filters

The detection filters affect the sensitivity of the Microhaplotype Caller (beta) (figure 10.8):

Image filters-detection
Figure 10.8: The Microhaplotype Caller detection filters.

Noise filters

These filter thresholds specify when a filter is applied to a genome element for it to be disregarded as noise (figure 10.9):

Image filters-noise
Figure 10.9: The Microhaplotype Caller noise filters.