The first steps of these workflows involve trimming off any remaining PCR adapters. This is followed by mapping the trimmed reads to the human reference sequence. The Structural Variant Caller then generates a guidance track that is used in the Local Realignment tool to improve the mapping.
For workflows designed to identify variants of interest, the improved mapping is then input to the Fixed Ploidy Variant Detection or Low Frequency Variant Detection tool. When applicable, the resulting variants are filtered to remove those located outside defined target regions. Remaining variants are then annotated with information such as the relation to repeat/homopolymer regions or gene elements. Finally, a series of filtering steps removes variants likely to be artifacts. The retained variants are output, along with reports and other associated results.