Variant Discovery parameters

Variant Discovery parameters control which variants are displayed by SeqMan Ultra. These parameters act as “soft” filters, meaning that they limit which variants appear in SeqMan Ultra reports without actually removing data from the project. If any of these values are changed after viewing the Variants view, SeqMan Ultra will re-run the report automatically and update the results.

To access the dialog, use Project > Project Parameters and click Variant Discovery on the left. Note that end-trimming parameters are not applicable to BAM-based projects or .assembly projects.

The Quality Score Threshold parameters limit which variants should be displayed based on quality scores.

• Minimum Score at SNP prevents bases with a quality score of less than the threshold value from being shown in the Variants view. The default Minimum Score at SNP is 5. At this setting, only bases with a quality score of greater than or equal to 5 will be shown in the Variants view. This parameter does not apply to variants that are gaps.

• Minimum Neighborhood Score prevents variants with a neighborhood quality score of less than the specified value from being displayed. Note that if the specified Neighborhood Window (see below) contains one or more mismatches to the reference sequence, the putative variant will be rejected, even if it meets the Minimum Neighborhood Score threshold.

• Neighborhood Window specifies the size of the window to be used when calculating the neighborhood quality score. For example, if this value is set to 5, then the 5 bases upstream and the 5 bases downstream from the variant base will be considered.

The Settings for Trace Files parameters establish the threshold for discovering heterozygous variant bases.

• The default for Heterozygous Peak Threshold is 50%, meaning any base that exhibits a secondary trace peak that is at least 50% of the intensity of the primary peak will be identified as heterozygous. A peak is defined as a trace that exhibits a negative curvature for the base. Lowering the value, and thus the stringency, increases the likelihood of bases being identified as putative variants by SeqMan Ultra. Setting the value to 100% turns off heterozygous variant detection and only the primary trace peak will be considered as a possible variant base. At 100%, only homozygous putative variants will be found by SeqMan Ultra.