Direction and position filters

Many sequencing protocols are prone to various types of amplification induced biases and errors. The 'Read direction' and 'Read position' filters are aimed at providing means for weeding out variants that are likely to originate from such biases.

Figure 27.24 shows an example of a variant that is removed by the 'Read direction' filter.

Image variantRemovedByReadDirectionFilterV1
Figure 27.24: An example of a variant that is filtered out by the Read Direction filter.

Note that variant calling was done ignoring non-specific matches and broken pair reads, so only the 16 intact paired reads (the blue reads) are considered. To see the direction of the reads, you must adjust the viewer settings in the 'Reads track' side panel, to 'Disconnect paired reads'. This has been done in figure 27.25. Now it becomes apparent that the variant is found in the forward reads (that is, the green reads) of the 16 intact paired reads, and in no reverse reads (except the three that come from broken pairs, and which were ignored), and therefore removed by the read direction data.

Image variantRemovedByReadDirectionFilterV2
Figure 27.25: The same data as shown in figure 27.24, but now with 'Disconnect paired reads' option switched on in the 'reads track' side panel.

Figure 27.26 shows an example of a variant that is removed by the read position filter, but not by the read direction filter. The variant is only present in a portion of the reads that cover the variant, and the portion or the reads that carry the variant have the variant occurring in read positions that are systematically different from what you would expect, given the general placement of reads covering the variant (e.g., none of the reads that start after position 186,641,600 carry the variant).

Image variantremovedbyreadpositionnotbyreaddirectionfilter
Figure 27.26: A variant that is filtered out by the Read position filter but not by the Read direction filter.