hg19 and GRCh38 human genome references

In Ion Reporter™ Software you can use human genome references hg19 or GRch38 for either pre-defined or custom workflows. You can use the Ion GRCh38 human reference when you create custom analysis workflows. The Ion GRCh38 Reference Genome in is based on the latest GRC human reference assembly and is the first major update since 2009. Highlights include changes to chromosome coordinates, fixed errors in the former sequence, addition of mitochondria, and multiple loci for some highly variable genes.

Ion AmpliSeq™ Designer currently offers one GRCh38 human reference and related target reference (BED) file for GRCh38 experiments. Optionally, you can also convert existing coordinates to GRCh38 by using a publicly available lift-over tool, such as CrossMap.

See the following topics for more information about custom analysis workflows:

• Steps in analysis workflow creation

• Create a custom analysis workflow from an existing analysis workflow

• Create a custom analysis workflow without predefined settings

• Create a copy number baseline workflow preset