In variant discovery, a known reference sequence is used for comparison with sample sequences. The reference sequence is often the wildtype sequence.
All bases identified by the SeqMan Pro variant discovery method as VARIANTs are initially evaluated as putative. Any base in a contig can be evaluated or re-evaluated as a putative variant, a confirmed variant, or a rejected variant.
Note: SeqMan Pro will automatically reject variants that occur within features of the type unsure. Please see Editing Features for information on how to change a feature type.
Adjacent variant positions are coalesced into multi-base insertions or deletions if both of these conditions are met:
•They are of the same type.
•At least 80% of the reads with the variant in one column have a called variant in the adjacent column.
To use SeqMan Pro’s variant discovery tools, first choose a reference sequence, and then display variants by selecting Variant > View Variants. Variants can be viewed from both the Strategy and Alignment Views, as well as using SeqMan Pro’s dynamic Variant Reports.
Note: Variants for BAM-based projects are not calculated by SeqMan Pro, but can be calculated during assembly by DNASTAR’s SeqMan NGen and then viewed in SeqMan Pro.