Low Frequency Variant Detection

As the Fixed Ploidy Variant Detection tool, the Low frequency variant Detection tool relies on

  1. A statistical model for the analyzed sample and
  2. A model for the sequencing errors.
The method employed in the Low Frequency Variant Detection tool for estimating the sequencing error rates is similar to that of the Fixed Ploidy Variant Detection tool (see The Error Model estimation), but the statistical model for the sample is different. It does not make any assumptions about the ploidy of the sample. Instead a statistical test is performed at each site to determine if the nucleotides observed in the reads at that site could be due simply to sequencing errors, or if they are significantly better explained by there being one (or more) alleles than the reference present in the sample at some unknown frequency. If the latter is the case, a variant corresponding to the significant allele will be called, with estimated frequency.

The Low Frequency Variant Detection tool has one parameter (figure 27.18):

The Low Frequency Variant Detection tool is suitable for analysis of samples of mixed tissue types (such as cancer 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. The tool also calls more abundant variants, and can be used for analysis of samples with ploidy larger than four. Note that, as the tool looks for all variants, abundant as well as low frequency ones, analysis will generally be slower than those of the other variant detection tools. In particular, it will be very slow, and possibly prohibitively so, for samples with extremely high coverage, or a very large number of variants (as in cases where the sample differs considerably from the reference).

Image lowfrequencyvariantdetectionparameters
Figure 27.18: The Low Frequency Variant Detection parameters.

For a more in depth description of the Low Frequency variant caller see Section 27.9.