Compatibility with CLC Genomics Workbench tools
Read mappings produced by the tools LightSpeed Fastq to Germline Variants, LightSpeed Fastq to Somatic Variants, and LightSpeed Fastq to Somatic Variants Tumor Normal differ in some fundamental ways from read mappings produced by the Map Reads to Reference tool. Read mappings produced by the tool LightSpeed Long Reads to Germline Variants (beta) also differ from read mappings produced by the Map Long Reads to Reference tool. The main differences are related to how base quality scores and unaligned ends are handled:
- Base quality scores The Lightspeed tools access and use the base quality scores during variant calling, but for efficiency reasons the base quality scores on the individual bases are not kept and stored on individual bases in the final read mapping. CLC Genomics Workbench tools that rely on quality scores being available on bases in a read mapping (such as the variant callers Fixed Ploidy Variant Detection and Low Frequency Variant Detection) cannot be expected to perform as well on a read mapping produced by a Lightspeed tool as on a read mapping produced with the Map Reads to Reference or the Map Long Reads to Reference tool available in CLC Genomics Workbench.
- Unaligned ends The LightSpeed tools for analyzing short reads include a structural variant detection step and a subsequent realignment step. In the structural variant detection step, structural variants are inferred from unaligned ends, and the realignment step uses the inferred structural variants during realignment. The realignment procedure differs from that used by the Local Realignment tool (available in CLC Genomics Workbench) in that unaligned ends that equally well support different alleles are kept unaligned. CLC Genomics Workbench tools that rely on unaligned ends in a read mapping (such as the InDels and Structural Variants tool) will therefore behave differently on a read mapping produced with these Lightspeed tools compared to a read mapping produced with the Map Reads to Reference tool. This difference does not apply to read mappings produced by LightSpeed Long Reads to Germline Variants (beta), which does not include a structural variant detection step.