Technology specific filters

Note that the higher you set the With frequency below parameter, the more variants will be removed. Figure 28.13 shows an example of a variant that is called when the pyro-error filter with minimum length setting 3 and frequency setting 0.5 is used, but that is filtered when the frequency setting is increased to 0.8. The variant has a frequency of 55.71.

Image pyrofilterremovedvariant
Figure 28.13: An example of a variant that is filtered out when the pyro-error filter is applied with settings 3 and 0.8, but not with settings 3 and 0.5.

In addition to the example above, a simple example is provided below in figure 28.14 to illustrate the difference between variant frequency and pyro-variant removal frequency (where non-reference and non-homopolymer variant reads are ignored).

Image simple_pyro-filter_example
Figure 28.14: An example of a simple read mapping with 6 mapped reads. Three of them indicate a deletion, two match the reference, and one read is an A to T SNP

The read with the T variant is not counted when calculating the frequency for the homopolymer deletion, because we only want to estimate how often a homopolymer variant appears for a given allele, and the T read is not from the same allele as the A and gap reads.

For the deletion, the variant frequency will be 50 percent, if it is reported. This is because it appears in 3 of 6 reads.

However, the pyro-variant removal frequency is 0.6, because it appears in 3 of 5 reads that come from the same allele. Thus the deletion will only be removed by the pyro-filter if the With frequency below parameter is above 0.6 and the In homopolymer regions with minimum length parameter is less than 7.